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

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2025 Workiva-->
<!--r:bb155796-0100-4249-80f6-c536ef2be3c2,g:5101a699-124c-42c6-a302-31b5af137804-->
<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-20250612.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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CoverAbstract"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentType_b583e500-de9f-4d32-b44b-5916a1b4325a" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_DocumentType_b583e500-de9f-4d32-b44b-5916a1b4325a" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentPeriodEndDate_f38b5122-574e-4822-8f03-f6c175cdb216" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_DocumentPeriodEndDate_f38b5122-574e-4822-8f03-f6c175cdb216" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityRegistrantName_1b6ac45e-3776-4a96-a2ca-25dd6bbd508b" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityRegistrantName_1b6ac45e-3776-4a96-a2ca-25dd6bbd508b" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityIncorporationStateCountryCode_35e35f17-4553-44eb-bb97-6a54d5fd6125" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityIncorporationStateCountryCode_35e35f17-4553-44eb-bb97-6a54d5fd6125" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityFileNumber_0b36c085-a20d-4fd0-924e-f0cd57a92f37" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityFileNumber_0b36c085-a20d-4fd0-924e-f0cd57a92f37" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityTaxIdentificationNumber_2ddf2b87-190f-4715-a8b9-486d16bf4eb0" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityTaxIdentificationNumber_2ddf2b87-190f-4715-a8b9-486d16bf4eb0" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressAddressLine1_14274e8d-71d2-491d-a74b-4185c299aa70" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityAddressAddressLine1_14274e8d-71d2-491d-a74b-4185c299aa70" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressAddressLine2_ae6bd8c2-17bd-46ad-9cf7-3c08d7e62f4e" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityAddressAddressLine2_ae6bd8c2-17bd-46ad-9cf7-3c08d7e62f4e" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressCityOrTown_b4d0f6cb-4e4b-4bd0-bdf9-7706e48f88df" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityAddressCityOrTown_b4d0f6cb-4e4b-4bd0-bdf9-7706e48f88df" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressStateOrProvince_920092d9-6985-4822-bb8b-8c20cc70824f" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityAddressStateOrProvince_920092d9-6985-4822-bb8b-8c20cc70824f" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressPostalZipCode_323ac334-defe-49ce-b819-fef9871c37d5" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityAddressPostalZipCode_323ac334-defe-49ce-b819-fef9871c37d5" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_CityAreaCode_57cc9452-069d-45a6-ab4e-a6750b0d0300" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_CityAreaCode_57cc9452-069d-45a6-ab4e-a6750b0d0300" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_LocalPhoneNumber_f09b777b-bb7d-4050-b1f5-f518e9d873d0" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_LocalPhoneNumber_f09b777b-bb7d-4050-b1f5-f518e9d873d0" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_WrittenCommunications_aabe264a-8dfe-4d0a-8a06-3e0334638562" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_WrittenCommunications_aabe264a-8dfe-4d0a-8a06-3e0334638562" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SolicitingMaterial_f679dcf7-9187-4a4b-bf65-e98112739cb1" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_SolicitingMaterial_f679dcf7-9187-4a4b-bf65-e98112739cb1" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementTenderOffer_e41db789-753d-446c-8a58-8855878376ce" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_PreCommencementTenderOffer_e41db789-753d-446c-8a58-8855878376ce" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementIssuerTenderOffer_bc767425-c04c-426f-b67c-0dc0c4e6d853" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_PreCommencementIssuerTenderOffer_bc767425-c04c-426f-b67c-0dc0c4e6d853" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_Security12bTitle_62276ba4-97f5-4f15-b112-03168e4dbbfb" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_Security12bTitle_62276ba4-97f5-4f15-b112-03168e4dbbfb" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_TradingSymbol_13a8eb4b-d07f-4a9a-a77f-c512db7e3639" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_TradingSymbol_13a8eb4b-d07f-4a9a-a77f-c512db7e3639" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SecurityExchangeName_a6409bd8-8c65-437d-966a-05bebe98551d" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_SecurityExchangeName_a6409bd8-8c65-437d-966a-05bebe98551d" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityEmergingGrowthCompany_b609e97f-69db-400c-942f-fe2cc8790ecb" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityEmergingGrowthCompany_b609e97f-69db-400c-942f-fe2cc8790ecb" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityCentralIndexKey_c1dc2fca-ec9a-4510-83f6-ee754da7ffe8" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_EntityCentralIndexKey_c1dc2fca-ec9a-4510-83f6-ee754da7ffe8" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_AmendmentFlag_9540d6b0-11ca-4801-ab7a-403c932db011" 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_422faf53-4495-44ff-9fde-b218211bb7f2" xlink:to="loc_dei_AmendmentFlag_9540d6b0-11ca-4801-ab7a-403c932db011" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
</link:linkbase>
