<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>
<periodOfReport>2004-01-06</periodOfReport>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000939767</issuerCik>
        <issuerName>EXELIXIS INC</issuerName>
        <issuerTradingSymbol>EXEL</issuerTradingSymbol>
</issuer>
<reportingOwner>
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            <rptOwnerCik>0001202102</rptOwnerCik>
            <rptOwnerName>SCANGOS GEORGE A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O EXELIXIS INC.</rptOwnerStreet1>
            <rptOwnerStreet2>170 HARBOR WAY, PO BOX 0511</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94083-0511</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
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<isOfficer>1</isOfficer>
<isTenPercentOwner>0</isTenPercentOwner>
<isOther>0</isOther>
<officerTitle>President, CEO &amp; Director</officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
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<value>Common Stock</value>
</securityTitle>
<transactionDate>
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<deemedExecutionDate>
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<transactionPricePerShare>
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</nonDerivativeTable>
<remarks></remarks>
<ownerSignature>
<signatureName>/s/ George Scangos</signatureName>
<signatureDate>2004-01-06</signatureDate>
</ownerSignature>
</ownershipDocument>

