<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2025 Workiva-->
<!--r:24221d43-244c-4e01-9a8d-26f87b9b86f1,g:266e9092-35f7-4aa4-a09e-2b7807e6acc7-->
<link:linkbase 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" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.vaxcyte.com/role/Cover" xlink:type="simple" xlink:href="pcvx-20250806.xsd#Cover"/>
  <link:presentationLink xlink:role="http://www.vaxcyte.com/role/Cover" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CoverAbstract"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentType_b6b3738d-3684-480f-9021-370abae88701" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentType"/>
    <link:presentationArc order="1" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_DocumentType_b6b3738d-3684-480f-9021-370abae88701" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentPeriodEndDate_037c1c3b-967a-471e-a0af-33dac86a4fa6" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentPeriodEndDate"/>
    <link:presentationArc order="2" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_DocumentPeriodEndDate_037c1c3b-967a-471e-a0af-33dac86a4fa6" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityRegistrantName_10cb9eb1-de3f-42a2-a95d-def770587dd9" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityRegistrantName"/>
    <link:presentationArc order="3" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityRegistrantName_10cb9eb1-de3f-42a2-a95d-def770587dd9" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityIncorporationStateCountryCode_0c2a9180-2511-4a78-a7ce-e064d66d89e8" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityIncorporationStateCountryCode"/>
    <link:presentationArc order="4" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityIncorporationStateCountryCode_0c2a9180-2511-4a78-a7ce-e064d66d89e8" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityFileNumber_27548bf5-9389-497a-973b-ccefda5428c3" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityFileNumber"/>
    <link:presentationArc order="5" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityFileNumber_27548bf5-9389-497a-973b-ccefda5428c3" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityTaxIdentificationNumber_2722aa62-0c88-489b-8ef2-ba43029e0766" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityTaxIdentificationNumber"/>
    <link:presentationArc order="6" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityTaxIdentificationNumber_2722aa62-0c88-489b-8ef2-ba43029e0766" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressAddressLine1_8e3ae5aa-78dc-4e67-84f0-0c5bed8dade6" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressAddressLine1"/>
    <link:presentationArc order="7" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityAddressAddressLine1_8e3ae5aa-78dc-4e67-84f0-0c5bed8dade6" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressAddressLine2_0f0c303a-f60f-4814-8153-1cdd35e995e1" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressAddressLine2"/>
    <link:presentationArc order="8" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityAddressAddressLine2_0f0c303a-f60f-4814-8153-1cdd35e995e1" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressCityOrTown_7fcb43b0-7ffe-4787-a5c7-c5ad86b2a7a4" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressCityOrTown"/>
    <link:presentationArc order="9" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityAddressCityOrTown_7fcb43b0-7ffe-4787-a5c7-c5ad86b2a7a4" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressStateOrProvince_e5088d67-81d7-4518-9b5e-37bfb90a1f4d" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressStateOrProvince"/>
    <link:presentationArc order="10" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityAddressStateOrProvince_e5088d67-81d7-4518-9b5e-37bfb90a1f4d" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressPostalZipCode_cdf79580-72aa-42d3-9466-25fb944e4d2f" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressPostalZipCode"/>
    <link:presentationArc order="11" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityAddressPostalZipCode_cdf79580-72aa-42d3-9466-25fb944e4d2f" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_CityAreaCode_bbb4bf0e-991f-4bf3-a4d8-dacf396d28f7" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CityAreaCode"/>
    <link:presentationArc order="12" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_CityAreaCode_bbb4bf0e-991f-4bf3-a4d8-dacf396d28f7" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_LocalPhoneNumber_3692d3ab-99bb-40d1-8693-022e8b98db10" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_LocalPhoneNumber"/>
    <link:presentationArc order="13" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_LocalPhoneNumber_3692d3ab-99bb-40d1-8693-022e8b98db10" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_WrittenCommunications_e9a382e7-6411-4bc8-9751-7ac5a811429c" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_WrittenCommunications"/>
    <link:presentationArc order="14" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_WrittenCommunications_e9a382e7-6411-4bc8-9751-7ac5a811429c" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SolicitingMaterial_f5a0c9ce-49df-4472-af97-e6216b11d15b" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_SolicitingMaterial"/>
    <link:presentationArc order="15" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_SolicitingMaterial_f5a0c9ce-49df-4472-af97-e6216b11d15b" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementTenderOffer_003f66cf-25e1-4de6-98ad-4f821d06a273" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_PreCommencementTenderOffer"/>
    <link:presentationArc order="16" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_PreCommencementTenderOffer_003f66cf-25e1-4de6-98ad-4f821d06a273" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementIssuerTenderOffer_eb2b15f2-8f3e-40ac-bcb8-26c26368c964" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_PreCommencementIssuerTenderOffer"/>
    <link:presentationArc order="17" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_PreCommencementIssuerTenderOffer_eb2b15f2-8f3e-40ac-bcb8-26c26368c964" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_Security12bTitle_c064cb8e-a9c8-4e00-9559-ace17f949a0d" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_Security12bTitle"/>
    <link:presentationArc order="18" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_Security12bTitle_c064cb8e-a9c8-4e00-9559-ace17f949a0d" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_TradingSymbol_67035b6f-49ee-404c-80f7-79b929860077" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_TradingSymbol"/>
    <link:presentationArc order="19" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_TradingSymbol_67035b6f-49ee-404c-80f7-79b929860077" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SecurityExchangeName_9ee6408b-1414-4e0b-928c-5ffc38808bf2" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_SecurityExchangeName"/>
    <link:presentationArc order="20" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_SecurityExchangeName_9ee6408b-1414-4e0b-928c-5ffc38808bf2" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityEmergingGrowthCompany_620fa6d7-f7c5-4864-9bd8-6a66f8ce1d58" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityEmergingGrowthCompany"/>
    <link:presentationArc order="21" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityEmergingGrowthCompany_620fa6d7-f7c5-4864-9bd8-6a66f8ce1d58" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityCentralIndexKey_3957a689-bdc5-4945-bbc9-c1dd215654c0" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityCentralIndexKey"/>
    <link:presentationArc order="22" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_EntityCentralIndexKey_3957a689-bdc5-4945-bbc9-c1dd215654c0" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_AmendmentFlag_a495ece8-8bb1-4227-8390-9303c97aff40" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AmendmentFlag"/>
    <link:presentationArc order="23" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_be9353e7-7a31-4e8a-acc1-f3f8c7c8cbaf" xlink:to="loc_dei_AmendmentFlag_a495ece8-8bb1-4227-8390-9303c97aff40" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
</link:linkbase>
