<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>4</documentType>
<periodOfReport>2003-06-18</periodOfReport>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000939767</issuerCik>
        <issuerName>EXELIXIS INC</issuerName>
        <issuerTradingSymbol>EXEL</issuerTradingSymbol>
</issuer>
<reportingOwner>
<reportingOwnerId>
            <rptOwnerCik>0001202102</rptOwnerCik>
            <rptOwnerName>SCANGOS GEORGE A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector>
<isOfficer>1</isOfficer>
<isTenPercentOwner>0</isTenPercentOwner>
<isOther>0</isOther>
<officerTitle>President, CEO and Director</officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<nonDerivativeSecurity>
<securityTitle>
<value>Common Stock</value>
<footnoteId id="F1"/>
</securityTitle>
<transactionDate>
<value>2003-06-18</value>
<footnoteId id="F1"/>
</transactionDate>
<deemedExecutionDate>
<value>2003-06-18</value>
<footnoteId id="F1"/>
</deemedExecutionDate>
<transactionCoding>
<transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
<footnoteId id="F1"/>
</transactionCoding>
<transactionTimeliness>
<value></value>
</transactionTimeliness>
<transactionAmounts>
<transactionShares>
<value>2500</value>
<footnoteId id="F1"/>
</transactionShares>
<transactionValue>
<value>8.1946</value>
<footnoteId id="F1"/>
</transactionValue>
<transactionAcquiredDisposedCode>
<value>D</value>
<footnoteId id="F1"/>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts>
<sharesOwnedFollowingTransaction>
<value>1836961</value>
<footnoteId id="F1"/>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature>
<directOrIndirectOwnership>
<value>D</value>
</directOrIndirectOwnership>
<natureOfOwnership>
<value></value>
</natureOfOwnership>
</ownershipNature>
</nonDerivativeSecurity>
<footnotes>
<footnote id="F1">Includes 1,865 shares of common stock acquired pursuant to Issuers ESPP on 4/30/02.</footnote>
</footnotes>
<ownerSignature>
<signatureName>George Scangos</signatureName>
<signatureDate>2003-06-20</signatureDate>
</ownerSignature>
</ownershipDocument>

