<?xml version="1.0" encoding="utf-8"?>
<!--Generated by DFIN XBRL Instance Document - http://www.dfinsolutions.com/ - Version R3.0 - on 09-April-2024 [09:56:17] {PM}-->
<schema targetNamespace="http://va.com/20231231" elementFormDefault="qualified" xmlns:pcvx="http://va.com/20231231" xmlns="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xl="http://www.xbrl.org/2003/XLink" xmlns:us-gaap="http://fasb.org/us-gaap/2023" xmlns:country="http://xbrl.sec.gov/country/2023" xmlns:dei="http://xbrl.sec.gov/dei/2023" xmlns:us-types="http://fasb.org/us-types/2023" xmlns:deprecated="http://www.xbrl.org/2009/arcrole/fact-explanatoryFact" xmlns:srt="http://fasb.org/srt/2023" xmlns:srt-types="http://fasb.org/srt-types/2023" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2020-01-21">
<annotation>
<appinfo>
<link:linkbaseRef xlink:type="simple" xlink:href="pcvx-20231231_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
<link:linkbaseRef xlink:type="simple" xlink:href="pcvx-20231231_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
<link:linkbaseRef xlink:type="simple" xlink:href="pcvx-20231231_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
</appinfo>
</annotation>
<import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd" />
<import namespace="http://www.xbrl.org/2003/linkbase" schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" />
<import namespace="http://xbrl.sec.gov/dei/2023" schemaLocation="https://xbrl.sec.gov/dei/2023/dei-2023.xsd" />
<import namespace="http://xbrl.sec.gov/dei-sub/2023" schemaLocation="https://xbrl.sec.gov/dei/2023/dei-sub-2023.xsd" />
<import namespace="http://www.xbrl.org/dtr/type/2020-01-21" schemaLocation="https://www.xbrl.org/dtr/type/2020-01-21/types.xsd" />
<import namespace="http://fasb.org/srt/2023" schemaLocation="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd" />
<import namespace="http://fasb.org/srt-types/2023" schemaLocation="https://xbrl.fasb.org/srt/2023/elts/srt-types-2023.xsd" />
<import namespace="http://xbrl.sec.gov/ecd-sub/2023" schemaLocation="https://xbrl.sec.gov/ecd/2023/ecd-sub-2023.xsd" />
<import namespace="http://xbrl.sec.gov/ecd/2023" schemaLocation="https://xbrl.sec.gov/ecd/2023/ecd-2023.xsd" />
<import namespace="http://www.xbrl.org/2006/ref" schemaLocation="http://www.xbrl.org/2006/ref-2006-02-27.xsd" />
<import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd" />
<import namespace="http://fasb.org/srt-roles/2023" schemaLocation="https://xbrl.fasb.org/srt/2023/elts/srt-roles-2023.xsd" />
<element name="AggregateValueForStockAwardsAndOptionAwardsIncludedInSctTotalForTheCoveredFiscalYearMember" type="dtr-types:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" id="pcvx_AggregateValueForStockAwardsAndOptionAwardsIncludedInSctTotalForTheCoveredFiscalYearMember" substitutionGroup="xbrli:item" />
<element name="ChangeAsOfTheVestingDateFromTheEndOfThePriorFiscalYearInFairValueOfAwardsGrantedInAnyPriorFiscalYearForWhichVestingConditionsWereSatisfiedDuringTheCoveredFiscalYearMember" type="dtr-types:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" id="pcvx_ChangeAsOfTheVestingDateFromTheEndOfThePriorFiscalYearInFairValueOfAwardsGrantedInAnyPriorFiscalYearForWhichVestingConditionsWereSatisfiedDuringTheCoveredFiscalYearMember" substitutionGroup="xbrli:item" />
<element name="FairValueAtYearEndOfAwardsGrantedDuringTheCoveredFiscalYearThatWereOutstandingAndUnvestedAtTheCoveredFiscalYearEndMember" type="dtr-types:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" id="pcvx_FairValueAtYearEndOfAwardsGrantedDuringTheCoveredFiscalYearThatWereOutstandingAndUnvestedAtTheCoveredFiscalYearEndMember" substitutionGroup="xbrli:item" />
<element name="VestingDateFairValueOfAwardsGrantedAndVestedDuringTheCoveredFiscalYearMember" type="dtr-types:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" id="pcvx_VestingDateFairValueOfAwardsGrantedAndVestedDuringTheCoveredFiscalYearMember" substitutionGroup="xbrli:item" />
<element name="YearOverYearChangeInFairValueAtCoveredFiscalYearEndOfAwardsGrantedInAnyPriorFiscalYearThatWereOutstandingAndUnvestedAtTheCoveredFiscalYearEndMember" type="dtr-types:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" id="pcvx_YearOverYearChangeInFairValueAtCoveredFiscalYearEndOfAwardsGrantedInAnyPriorFiscalYearThatWereOutstandingAndUnvestedAtTheCoveredFiscalYearEndMember" substitutionGroup="xbrli:item" />
</schema>
