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<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2021-03-28T21:49:53.3567111+00:00 -->
<!-- Version            : 5.0.1.571 -->
<!-- Package ID         : ad55114987544809b63c9baee2a250f1 -->
<!-- Copyright (c) 2021 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="pcvx_AccruedResearchAndDevelopmentPolicyTextBlock" name="AccruedResearchAndDevelopmentPolicyTextBlock" type="nonnum:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_ScheduleOfCommonStockSharesReservedForFutureIssuanceTableTextBlock" name="ScheduleOfCommonStockSharesReservedForFutureIssuanceTableTextBlock" type="nonnum:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_TwoThousandTwentyEquityIncentivePlanAndTwoThousandFourteenEquityIncentivePlanMember" name="TwoThousandTwentyEquityIncentivePlanAndTwoThousandFourteenEquityIncentivePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_TwoThousandTwentyEmployeeStockPurchasePlanMember" name="TwoThousandTwentyEmployeeStockPurchasePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_TwoThousandFourteenEquityIncentivePlanAndTwoThousandTwentyEquityIncentivePlanAndTwoThousandTwentyEmployeeStockPurchasePlanMember" name="TwoThousandFourteenEquityIncentivePlanAndTwoThousandTwentyEquityIncentivePlanAndTwoThousandTwentyEmployeeStockPurchasePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_GlobalTargetRevenue" name="GlobalTargetRevenue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_ScheduleOfOrganizationConsolidationAndPresentationOfFinancialStatementsLineItems" name="ScheduleOfOrganizationConsolidationAndPresentationOfFinancialStatementsLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_ScheduleOfOrganizationConsolidationAndPresentationOfFinancialStatementsTable" name="ScheduleOfOrganizationConsolidationAndPresentationOfFinancialStatementsTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_PneumococcalConjugateVaccineMember" name="PneumococcalConjugateVaccineMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_SharesIssuedUponFullExerciseOfUnderwritersOptionToPurchaseAdditionalShares" name="SharesIssuedUponFullExerciseOfUnderwritersOptionToPurchaseAdditionalShares" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_PaymentsOfUnderwritingDiscountsAndCommissions" name="PaymentsOfUnderwritingDiscountsAndCommissions" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_InitialPublicOfferingRelatedCost" name="InitialPublicOfferingRelatedCost" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="pcvx_WarrantLiabilityMember" name="WarrantLiabilityMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_PreferredStockWarrantOutstandingMeasurementInput" name="PreferredStockWarrantOutstandingMeasurementInput" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="pcvx_RedeemableConvertiblePreferredStockWarrantMember" name="RedeemableConvertiblePreferredStockWarrantMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_RedeemableConvertiblePreferredStockWarrantLiabilityMember" name="RedeemableConvertiblePreferredStockWarrantLiabilityMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_ComputersAndComputerSoftwareMember" name="ComputersAndComputerSoftwareMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_LabEquipmentMember" name="LabEquipmentMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_CapitalLeasesLabEquipmentMember" name="CapitalLeasesLabEquipmentMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_AccruedPreclinicalStudiesCurrent" name="AccruedPreclinicalStudiesCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_LesseeFinanceLeaseInterestRate" name="LesseeFinanceLeaseInterestRate" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="pcvx_LonzaLimitedMember" name="LonzaLimitedMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_PercentageOfAnnualRentalPaymentsIncludingGuaranteedResidualValue" name="PercentageOfAnnualRentalPaymentsIncludingGuaranteedResidualValue" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_NumberOfLabEquipment" name="NumberOfLabEquipment" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_LesseeOperatingLeaseExtendedLeaseTerm" name="LesseeOperatingLeaseExtendedLeaseTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_LesseeOperatingLeaseExpectedPaymentsOverLeaseTerm" name="LesseeOperatingLeaseExpectedPaymentsOverLeaseTerm" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_LesseeOperatingLeaseCommencementDate" name="LesseeOperatingLeaseCommencementDate" type="xbrli:dateItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_LesseeOperatingLeaseRenewalOption" name="LesseeOperatingLeaseRenewalOption" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_LesseeOperatingLeaseRentCommencementTerm" name="LesseeOperatingLeaseRentCommencementTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_DevelopmentAndManufacturingServicesAgreementEquityPaymentsPercentage" name="DevelopmentAndManufacturingServicesAgreementEquityPaymentsPercentage" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_DevelopmentAndManufacturingServicesAgreementPaymentsInEquity" name="DevelopmentAndManufacturingServicesAgreementPaymentsInEquity" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_ThresholdLimitOnEquityPayments" name="ThresholdLimitOnEquityPayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_SeriesDRedeemableConvertiblePreferredStockMember" name="SeriesDRedeemableConvertiblePreferredStockMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_ConversionOfRedeemableConvertiblePreferredStockMember" name="ConversionOfRedeemableConvertiblePreferredStockMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_SharesAvailableForFutureStockOptionGrantsMember" name="SharesAvailableForFutureStockOptionGrantsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_ClassOfWarrantOrRightNumberOfSecuritiesCalledByEachWarrantOrRightExercised" name="ClassOfWarrantOrRightNumberOfSecuritiesCalledByEachWarrantOrRightExercised" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="pcvx_CommonStockWarrantMember" name="CommonStockWarrantMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_ClassOfWarrantOrRightIssueDate" name="ClassOfWarrantOrRightIssueDate" type="xbrli:dateItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_IncentiveStockOptionGrantedToEmployeesOwningPercentageOfSharesOfCommonStock" name="IncentiveStockOptionGrantedToEmployeesOwningPercentageOfSharesOfCommonStock" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_PercentageOfFairValuePerShareOnTheGrantDate" name="PercentageOfFairValuePerShareOnTheGrantDate" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_ExercisePriceExpireInYearsFormTheDateOfGrant" name="ExercisePriceExpireInYearsFormTheDateOfGrant" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_StockOptionsGrantedTerm" name="StockOptionsGrantedTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_PercentageOfProvisionsSubjectToStockholders" name="PercentageOfProvisionsSubjectToStockholders" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesIncreaseInAvailableForGrant" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesIncreaseInAvailableForGrant" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_TwoThousandTwentyEquityIncentivePlanMember" name="TwoThousandTwentyEquityIncentivePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_TwoThousandFourteenEquityIncentivePlanMember" name="TwoThousandFourteenEquityIncentivePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_EarlyExercisedStockOptions" name="EarlyExercisedStockOptions" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="pcvx_RemainingLiabilitiesRelatedToEarlyExercisedShares" name="RemainingLiabilitiesRelatedToEarlyExercisedShares" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrantGrantedInPeriod" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrantGrantedInPeriod" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrantExercisedInPeriod" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrantExercisedInPeriod" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrantForfeitedInPeriod" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrantForfeitedInPeriod" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_OfferingPeriod" name="OfferingPeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_PurchasePeriod" name="PurchasePeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_FundingPeriodOfAwardToDevelopUniversalVaccineToPreventInfections" name="FundingPeriodOfAwardToDevelopUniversalVaccineToPreventInfections" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_PercentageOfReimbursableExpenses" name="PercentageOfReimbursableExpenses" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_InitialFundingCommittedByAward" name="InitialFundingCommittedByAward" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_FundingCommittedByAwardAvailableUponAchievementOfDevelopmentMilestones" name="FundingCommittedByAwardAvailableUponAchievementOfDevelopmentMilestones" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="pcvx_FundingArrangementLineItems" name="FundingArrangementLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_FundingArrangementTable" name="FundingArrangementTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_CostReimbursementSubAwardAgreementMember" name="CostReimbursementSubAwardAgreementMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_CombatingAntibioticResistantBacteriaBiopharmaceuticalAcceleratorAgreementMember" name="CombatingAntibioticResistantBacteriaBiopharmaceuticalAcceleratorAgreementMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_EffectiveIncomeTaxRateReconciliationChangeInFairValueOfTrancheLiability" name="EffectiveIncomeTaxRateReconciliationChangeInFairValueOfTrancheLiability" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_DeferredTaxAssetsTaxAccruedManufacturingExpenses" name="DeferredTaxAssetsTaxAccruedManufacturingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="pcvx_OperatingLossCarryForwardsExpirationYear" name="OperatingLossCarryForwardsExpirationYear" type="xbrli:gYearItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_IncomeTaxDisclosureLineItems" name="IncomeTaxDisclosureLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_IncomeTaxDisclosureTable" name="IncomeTaxDisclosureTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_TaxCreditCarryforwardExpirationYear" name="TaxCreditCarryforwardExpirationYear" type="xbrli:gYearItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="pcvx_SutroBiopharmaIncMember" name="SutroBiopharmaIncMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_PreferredStockWarrantMember" name="PreferredStockWarrantMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_LicenseAmendmentATwoMember" name="LicenseAmendmentATwoMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_LicenseAgreementMember" name="LicenseAgreementMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_SupplyAgreementMember" name="SupplyAgreementMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="pcvx_PercentageOfRoyaltyPaymentOnAnnualNetSalesOfVaccineProductsForHumanHealth" name="PercentageOfRoyaltyPaymentOnAnnualNetSalesOfVaccineProductsForHumanHealth" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="pcvx_PercentageOfRoyaltyPaymentOnNetSalesOfVaccineCompositionsForAnimalHealth" name="PercentageOfRoyaltyPaymentOnNetSalesOfVaccineCompositionsForAnimalHealth" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
</xsd:schema>
