<?xml version="1.0" encoding="US-ASCII"?>
<!-- DFIN New ActiveDisclosure (SM) XBRL Linkbase Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date :2022-02-28T14:49:03.5996+00:00 -->
<!-- Copyright (c) 2022 Donnelly Financial Solutions, Inc. All Rights Reserved. -->
<link:linkbase xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementBalanceSheets" xlink:href="pcvx-20211231.xsd#Role_StatementBalanceSheets" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementStatementsOfOperations" xlink:href="pcvx-20211231.xsd#Role_StatementStatementsOfOperations" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementStatementsOfComprehensiveLoss" xlink:href="pcvx-20211231.xsd#Role_StatementStatementsOfComprehensiveLoss" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementStatementsOfCashFlowsUnaudited" xlink:href="pcvx-20211231.xsd#Role_StatementStatementsOfCashFlowsUnaudited" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/DisclosureBasisOfPresentationAndSummaryOfSignificantAccountingPoliciesScheduleOfCashCashEquivalentsAndRestrictedCashDetails" xlink:href="pcvx-20211231.xsd#DisclosureBasisOfPresentationAndSummaryOfSignificantAccountingPoliciesScheduleOfCashCashEquivalentsAndRestrictedCashDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureFairValueMeasurementsAndFairValueOfFinancialInstrumentsScheduleOfFinancialInstrumentsMeasuredAtFairValueOnRecurringBasisDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureFairValueMeasurementsAndFairValueOfFinancialInstrumentsScheduleOfFinancialInstrumentsMeasuredAtFairValueOnRecurringBasisDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureFairValueMeasurementsAndFairValueOfFinancialInstrumentsScheduleOfContractualMaturitiesOfInvestmentsDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureFairValueMeasurementsAndFairValueOfFinancialInstrumentsScheduleOfContractualMaturitiesOfInvestmentsDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureBalanceSheetDetailsScheduleOfPropertyAndEquipmentNetDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureBalanceSheetDetailsScheduleOfPropertyAndEquipmentNetDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureBalanceSheetDetailsScheduleOfAccruedExpensesDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureBalanceSheetDetailsScheduleOfAccruedExpensesDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureLeasesScheduleOfInformationRelatedToROUAssetsAndLeaseLiabilitiesDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureLeasesScheduleOfInformationRelatedToROUAssetsAndLeaseLiabilitiesDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureLeasesScheduleOfMaturitiesOfLeaseLiabilitiesDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureLeasesScheduleOfMaturitiesOfLeaseLiabilitiesDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureLeasesScheduleOfMaturitiesOfLeaseLiabilitiesDetails2" xlink:href="pcvx-20211231.xsd#Role_DisclosureLeasesScheduleOfMaturitiesOfLeaseLiabilitiesDetails2" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureIncomeTaxesReconciliationOfEffectiveTaxRateDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureIncomeTaxesReconciliationOfEffectiveTaxRateDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureIncomeTaxesComponentsOfDeferredTaxAssetsDetails" xlink:href="pcvx-20211231.xsd#Role_DisclosureIncomeTaxesComponentsOfDeferredTaxAssetsDetails" xlink:type="simple"/>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementBalanceSheets">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_Liabilities" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AssetsCurrent" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_PreferredStockValue" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_LiabilitiesCurrent" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsNoncurrent" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccountsPayableCurrent" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AssetsNoncurrent" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_DeferredRentCreditNoncurrent" order="1" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_CommitmentsAndContingencies" order="1" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_EmployeeRelatedLiabilitiesCurrent" order="1" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_ShortTermInvestments" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_CommonStockValue" order="1" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsNoncurrent" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" order="2" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" order="2" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_StockholdersEquity" order="2" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsNoncurrent" xlink:to="us-gaap_LongTermInvestments" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="pcvx_AccruedManufacturingExpenses" order="2" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="3" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_OtherLiabilitiesNoncurrent" order="3" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" order="3" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsNoncurrent" xlink:to="us-gaap_RestrictedCashNoncurrent" order="3" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_DeferredRentCreditCurrent" order="4" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsNoncurrent" xlink:to="us-gaap_OtherAssetsNoncurrent" order="4" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="4" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" order="5" weight="1" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_Liabilities" xlink:label="us-gaap_Liabilities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_Assets" xlink:label="us-gaap_Assets"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AssetsCurrent" xlink:label="us-gaap_AssetsCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PreferredStockValue" xlink:label="us-gaap_PreferredStockValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:label="us-gaap_LiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AssetsNoncurrent" xlink:label="us-gaap_AssetsNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:label="us-gaap_AccountsPayableCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredRentCreditNoncurrent" xlink:label="us-gaap_DeferredRentCreditNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_CommitmentsAndContingencies" xlink:label="us-gaap_CommitmentsAndContingencies"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:label="us-gaap_EmployeeRelatedLiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ShortTermInvestments" xlink:label="us-gaap_ShortTermInvestments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LongTermInvestments" xlink:label="us-gaap_LongTermInvestments"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_AccruedManufacturingExpenses" xlink:label="pcvx_AccruedManufacturingExpenses"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OtherLiabilitiesNoncurrent" xlink:label="us-gaap_OtherLiabilitiesNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_RestrictedCashNoncurrent" xlink:label="us-gaap_RestrictedCashNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredRentCreditCurrent" xlink:label="us-gaap_DeferredRentCreditCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OtherAssetsNoncurrent" xlink:label="us-gaap_OtherAssetsNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementStatementsOfOperations">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherNonoperatingIncomeExpense" xlink:to="us-gaap_InterestExpense" order="0" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OperatingIncomeLoss" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="us-gaap_ResearchAndDevelopmentExpense" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_OperatingExpenses" order="0" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherNonoperatingIncomeExpense" xlink:to="us-gaap_InvestmentIncomeInterest" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="us-gaap_GeneralAndAdministrativeExpense" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherNonoperatingIncomeExpense" xlink:to="pcvx_GrantIncome" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherNonoperatingIncomeExpense" xlink:to="us-gaap_MarketableSecuritiesRealizedGainLoss" order="3" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherNonoperatingIncomeExpense" xlink:to="us-gaap_ForeignCurrencyTransactionGainLossBeforeTax" order="4" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherNonoperatingIncomeExpense" xlink:to="pcvx_ChangeInFairValueOfRedeemableConvertiblePreferredStock" order="5" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:label="us-gaap_OtherNonoperatingIncomeExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_InterestExpense" xlink:label="us-gaap_InterestExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingIncomeLoss" xlink:label="us-gaap_OperatingIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingExpenses" xlink:label="us-gaap_OperatingExpenses"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:label="us-gaap_ResearchAndDevelopmentExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_InvestmentIncomeInterest" xlink:label="us-gaap_InvestmentIncomeInterest"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:label="us-gaap_GeneralAndAdministrativeExpense"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_GrantIncome" xlink:label="pcvx_GrantIncome"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_MarketableSecuritiesRealizedGainLoss" xlink:label="us-gaap_MarketableSecuritiesRealizedGainLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ForeignCurrencyTransactionGainLossBeforeTax" xlink:label="us-gaap_ForeignCurrencyTransactionGainLossBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_ChangeInFairValueOfRedeemableConvertiblePreferredStock" xlink:label="pcvx_ChangeInFairValueOfRedeemableConvertiblePreferredStock"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementStatementsOfComprehensiveLoss">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_NetIncomeLoss" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodBeforeTax" order="1" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodBeforeTax" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodBeforeTax"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_StatementStatementsOfCashFlowsUnaudited">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="0" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_ProfitLoss" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="pcvx_PaymentsOfCapitalLeaseObligations" order="0" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" order="1" weight="-1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_DepreciationDepletionAndAmortization" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="pcvx_ProceedsFromInitialPublicOfferingNetOfUnderwritersCommissionsAndDiscounts" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_ShareBasedCompensation" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" order="2" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_PaymentsOfStockIssuanceCosts" order="2" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents" order="3" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromIssuanceOfRedeemableConvertiblePreferredStock" order="3" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_ProceedsFromSaleOfAvailableForSaleSecuritiesDebt" order="3" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="pcvx_ExpenseOnIssuanceOfRedeemableConvertiblePreferredStockWarrant" order="3" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_FairValueAdjustmentOfWarrants" order="4" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" order="4" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromStockOptionsExercised" order="4" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" order="5" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="pcvx_ChangeInFairValueOfRedeemableConvertiblePreferredStockTrancheLiabilities" order="5" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="pcvx_ProceedsFromIssuanceOfCommonStockRelatedToEarlyExercisedStockOptions" order="6" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_GainLossOnDispositionOfAssets1" order="6" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_AssetImpairmentCharges" order="7" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromStockPlans" order="7" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense" order="8" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="pcvx_PaymentOfDeferredOfferingCosts" order="8" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" order="9" weight="-1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" order="10" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInOtherOperatingAssets" order="11" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="pcvx_IncreaseDecreaseInOperatingLeaseLiabilities" order="12" weight="-1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayable" order="13" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="pcvx_IncreaseDecreaseInAccruedCompensation" order="14" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="pcvx_IncreaseDecreaseInAccruedManufacturingExpenses" order="15" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccruedLiabilities" order="16" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="pcvx_IncreaseDecreaseInAccruedLegalSettlement" order="17" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="pcvx_IncreaseDecreaseInDeferredRentAndOtherLongTermLiabilities" order="18" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProfitLoss" xlink:label="us-gaap_ProfitLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_PaymentsOfCapitalLeaseObligations" xlink:label="pcvx_PaymentsOfCapitalLeaseObligations"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" xlink:label="us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DepreciationDepletionAndAmortization" xlink:label="us-gaap_DepreciationDepletionAndAmortization"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_ProceedsFromInitialPublicOfferingNetOfUnderwritersCommissionsAndDiscounts" xlink:label="pcvx_ProceedsFromInitialPublicOfferingNetOfUnderwritersCommissionsAndDiscounts"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" xlink:label="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PaymentsOfStockIssuanceCosts" xlink:label="us-gaap_PaymentsOfStockIssuanceCosts"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents" xlink:label="us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProceedsFromIssuanceOfRedeemableConvertiblePreferredStock" xlink:label="us-gaap_ProceedsFromIssuanceOfRedeemableConvertiblePreferredStock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProceedsFromSaleOfAvailableForSaleSecuritiesDebt" xlink:label="us-gaap_ProceedsFromSaleOfAvailableForSaleSecuritiesDebt"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_ExpenseOnIssuanceOfRedeemableConvertiblePreferredStockWarrant" xlink:label="pcvx_ExpenseOnIssuanceOfRedeemableConvertiblePreferredStockWarrant"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_FairValueAdjustmentOfWarrants" xlink:label="us-gaap_FairValueAdjustmentOfWarrants"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" xlink:label="us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProceedsFromStockOptionsExercised" xlink:label="us-gaap_ProceedsFromStockOptionsExercised"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_ChangeInFairValueOfRedeemableConvertiblePreferredStockTrancheLiabilities" xlink:label="pcvx_ChangeInFairValueOfRedeemableConvertiblePreferredStockTrancheLiabilities"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_ProceedsFromIssuanceOfCommonStockRelatedToEarlyExercisedStockOptions" xlink:label="pcvx_ProceedsFromIssuanceOfCommonStockRelatedToEarlyExercisedStockOptions"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_GainLossOnDispositionOfAssets1" xlink:label="us-gaap_GainLossOnDispositionOfAssets1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AssetImpairmentCharges" xlink:label="us-gaap_AssetImpairmentCharges"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_ProceedsFromStockPlans" xlink:label="us-gaap_ProceedsFromStockPlans"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense" xlink:label="us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_PaymentOfDeferredOfferingCosts" xlink:label="pcvx_PaymentOfDeferredOfferingCosts"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" xlink:label="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_IncreaseDecreaseInOtherOperatingAssets" xlink:label="us-gaap_IncreaseDecreaseInOtherOperatingAssets"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_IncreaseDecreaseInOperatingLeaseLiabilities" xlink:label="pcvx_IncreaseDecreaseInOperatingLeaseLiabilities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsPayable" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayable"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_IncreaseDecreaseInAccruedCompensation" xlink:label="pcvx_IncreaseDecreaseInAccruedCompensation"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_IncreaseDecreaseInAccruedManufacturingExpenses" xlink:label="pcvx_IncreaseDecreaseInAccruedManufacturingExpenses"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilities" xlink:label="us-gaap_IncreaseDecreaseInAccruedLiabilities"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_IncreaseDecreaseInAccruedLegalSettlement" xlink:label="pcvx_IncreaseDecreaseInAccruedLegalSettlement"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_IncreaseDecreaseInDeferredRentAndOtherLongTermLiabilities" xlink:label="pcvx_IncreaseDecreaseInDeferredRentAndOtherLongTermLiabilities"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/DisclosureBasisOfPresentationAndSummaryOfSignificantAccountingPoliciesScheduleOfCashCashEquivalentsAndRestrictedCashDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents" xlink:to="us-gaap_RestrictedCash" order="1" weight="1" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_RestrictedCash" xlink:label="us-gaap_RestrictedCash"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureFairValueMeasurementsAndFairValueOfFinancialInstrumentsScheduleOfFinancialInstrumentsMeasuredAtFairValueOnRecurringBasisDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="0" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis" xlink:to="pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax" order="0" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_CashAndCashEquivalentsAmortizedCost" xlink:to="pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax" order="0" weight="-1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_CashAndCashEquivalentsAmortizedCost" xlink:to="pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis" xlink:to="pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_CashAndCashEquivalentsAmortizedCost" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis" xlink:to="pcvx_CashAndCashEquivalentsAndInvestments" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" order="2" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis" xlink:label="pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax" xlink:label="pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_CashAndCashEquivalentsAmortizedCost" xlink:label="pcvx_CashAndCashEquivalentsAmortizedCost"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax" xlink:label="pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax" xlink:label="pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax" xlink:label="pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_CashAndCashEquivalentsAndInvestments" xlink:label="pcvx_CashAndCashEquivalentsAndInvestments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureFairValueMeasurementsAndFairValueOfFinancialInstrumentsScheduleOfContractualMaturitiesOfInvestmentsDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearFairValue" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughFiveYearsFairValue" order="1" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearFairValue" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearFairValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughFiveYearsFairValue" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughFiveYearsFairValue"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureBalanceSheetDetailsScheduleOfPropertyAndEquipmentNetDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentNet" xlink:to="us-gaap_PropertyPlantAndEquipmentGross" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentNet" xlink:to="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" order="1" weight="-1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_PropertyPlantAndEquipmentGross" xlink:label="us-gaap_PropertyPlantAndEquipmentGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" xlink:label="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureBalanceSheetDetailsScheduleOfAccruedExpensesDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="pcvx_AccruedPreclinicalStudiesCurrent" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_AccruedProfessionalFeesCurrent" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_OtherAccruedLiabilitiesCurrent" order="2" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_AccruedPreclinicalStudiesCurrent" xlink:label="pcvx_AccruedPreclinicalStudiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_AccruedProfessionalFeesCurrent" xlink:label="us-gaap_AccruedProfessionalFeesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OtherAccruedLiabilitiesCurrent" xlink:label="us-gaap_OtherAccruedLiabilitiesCurrent"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureLeasesScheduleOfInformationRelatedToROUAssetsAndLeaseLiabilitiesDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLiability" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLiability" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" order="1" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseLiability" xlink:label="us-gaap_OperatingLeaseLiability"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureLeasesScheduleOfMaturitiesOfLeaseLiabilitiesDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="pcvx_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonthsNetOfLeaseIncentives" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" order="3" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" order="4" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="pcvx_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFour" order="5" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonthsNetOfLeaseIncentives" xlink:label="pcvx_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonthsNetOfLeaseIncentives"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFour" xlink:label="pcvx_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFour"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureLeasesScheduleOfMaturitiesOfLeaseLiabilitiesDetails2">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_OperatingLeaseLiability" order="1" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_OperatingLeaseLiability" xlink:label="us-gaap_OperatingLeaseLiability"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureIncomeTaxesReconciliationOfEffectiveTaxRateDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationAtFederalStatutoryIncomeTaxRate" order="0" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationNondeductibleExpenseShareBasedCompensationCost" order="1" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationTaxCredits" order="2" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="pcvx_EffectiveIncomeTaxRateReconciliationChangeInFairValueOfTrancheLiability" order="3" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="pcvx_Section162MLimitation" order="4" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationOtherAdjustments" order="5" weight="1.00" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationChangeInDeferredTaxAssetsValuationAllowance" order="6" weight="1.00" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:label="us-gaap_EffectiveIncomeTaxRateContinuingOperations"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationAtFederalStatutoryIncomeTaxRate" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationAtFederalStatutoryIncomeTaxRate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationNondeductibleExpenseShareBasedCompensationCost" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationNondeductibleExpenseShareBasedCompensationCost"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationTaxCredits" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationTaxCredits"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_EffectiveIncomeTaxRateReconciliationChangeInFairValueOfTrancheLiability" xlink:label="pcvx_EffectiveIncomeTaxRateReconciliationChangeInFairValueOfTrancheLiability"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_Section162MLimitation" xlink:label="pcvx_Section162MLimitation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationOtherAdjustments" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationOtherAdjustments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationChangeInDeferredTaxAssetsValuationAllowance" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationChangeInDeferredTaxAssetsValuationAllowance"/>
  </link:calculationLink>
  <link:calculationLink xlink:type="extended" xlink:role="http://www.vaxcyte.com/20211231/taxonomy/role/Role_DisclosureIncomeTaxesComponentsOfDeferredTaxAssetsDetails">
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredIncomeTaxLiabilities" xlink:to="us-gaap_DeferredTaxLiabilitiesLeasingArrangements" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsOperatingLossCarryforwards" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_DeferredTaxAssetsLiabilitiesNetBeforeValuationAllowance" xlink:to="us-gaap_DeferredTaxAssetsGross" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsLiabilitiesNet" xlink:to="pcvx_DeferredTaxAssetsLiabilitiesNetBeforeValuationAllowance" order="0" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="pcvx_DeferredTaxAssetsLiabilitiesNetBeforeValuationAllowance" xlink:to="us-gaap_DeferredIncomeTaxLiabilities" order="1" weight="-1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsLiabilitiesNet" xlink:to="us-gaap_DeferredTaxAssetsValuationAllowance" order="1" weight="-1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsPropertyPlantAndEquipment" order="1" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsTaxDeferredExpenseReservesAndAccruals" order="2" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsTaxCreditCarryforwards" order="3" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsInProcessResearchAndDevelopment" order="4" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="pcvx_DeferredTaxAssetsTaxAccruedManufacturingExpenses" order="5" weight="1" use="optional"/>
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="pcvx_LeaseLiability" order="6" weight="1" use="optional"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredIncomeTaxLiabilities" xlink:label="us-gaap_DeferredIncomeTaxLiabilities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxLiabilitiesLeasingArrangements" xlink:label="us-gaap_DeferredTaxLiabilitiesLeasingArrangements"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsGross" xlink:label="us-gaap_DeferredTaxAssetsGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsOperatingLossCarryforwards" xlink:label="us-gaap_DeferredTaxAssetsOperatingLossCarryforwards"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_DeferredTaxAssetsLiabilitiesNetBeforeValuationAllowance" xlink:label="pcvx_DeferredTaxAssetsLiabilitiesNetBeforeValuationAllowance"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsLiabilitiesNet" xlink:label="us-gaap_DeferredTaxAssetsLiabilitiesNet"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsValuationAllowance" xlink:label="us-gaap_DeferredTaxAssetsValuationAllowance"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsPropertyPlantAndEquipment" xlink:label="us-gaap_DeferredTaxAssetsPropertyPlantAndEquipment"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsTaxDeferredExpenseReservesAndAccruals" xlink:label="us-gaap_DeferredTaxAssetsTaxDeferredExpenseReservesAndAccruals"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsTaxCreditCarryforwards" xlink:label="us-gaap_DeferredTaxAssetsTaxCreditCarryforwards"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd#us-gaap_DeferredTaxAssetsInProcessResearchAndDevelopment" xlink:label="us-gaap_DeferredTaxAssetsInProcessResearchAndDevelopment"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_DeferredTaxAssetsTaxAccruedManufacturingExpenses" xlink:label="pcvx_DeferredTaxAssetsTaxAccruedManufacturingExpenses"/>
    <link:loc xlink:type="locator" xlink:href="pcvx-20211231.xsd#pcvx_LeaseLiability" xlink:label="pcvx_LeaseLiability"/>
  </link:calculationLink>
</link:linkbase>
