<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0304</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2012-02-01</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000911326</issuerCik>
        <issuerName>SYNAGEVA BIOPHARMA CORP</issuerName>
        <issuerTradingSymbol>GEVA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001111794</rptOwnerCik>
            <rptOwnerName>TISCH DANIEL R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>500 PARK AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

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                <value>Common Stock</value>
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            </transactionDate>
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                <equitySwapInvolved>0</equitySwapInvolved>
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                <transactionPricePerShare>
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                </transactionPricePerShare>
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                    <value>D</value>
                </transactionAcquiredDisposedCode>
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                    <value>304101</value>
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                <directOrIndirectOwnership>
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            </securityTitle>
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                <directOrIndirectOwnership>
                    <value>I</value>
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                    <value>Through trusts</value>
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        <nonDerivativeHolding>
            <securityTitle>
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                <sharesOwnedFollowingTransaction>
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                <transactionShares>
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            <securityTitle>
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                <value>Common Stock</value>
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            <securityTitle>
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                </transactionShares>
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                    <value>37.34</value>
                </transactionPricePerShare>
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                    <value>D</value>
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                <sharesOwnedFollowingTransaction>
                    <value>199400</value>
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                <directOrIndirectOwnership>
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            <securityTitle>
                <value>Common Stock</value>
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                <directOrIndirectOwnership>
                    <value>I</value>
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                <natureOfOwnership>
                    <value>Through family partnership</value>
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        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
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                <sharesOwnedFollowingTransaction>
                    <value>235557</value>
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                <directOrIndirectOwnership>
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            <securityTitle>
                <value>Common Stock</value>
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                <transactionCode>S</transactionCode>
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            <transactionAmounts>
                <transactionShares>
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                </transactionShares>
                <transactionPricePerShare>
                    <value>38.01</value>
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                    <value>D</value>
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                <sharesOwnedFollowingTransaction>
                    <value>183650</value>
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                <directOrIndirectOwnership>
                    <value>I</value>
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                <natureOfOwnership>
                    <value>Through trusts</value>
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        <nonDerivativeHolding>
            <securityTitle>
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                    <value>Through family partnership</value>
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            <securityTitle>
                <value>Common Stock</value>
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                    <value>235557</value>
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                <directOrIndirectOwnership>
                    <value>D</value>
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            <securityTitle>
                <value>Common Stock</value>
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                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
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                    <value>9190</value>
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                    <value>D</value>
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                    <value>174460</value>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Through trusts</value>
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        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
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                <sharesOwnedFollowingTransaction>
                    <value>59262</value>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Through family partnership</value>
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            <securityTitle>
                <value>Common Stock</value>
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                <sharesOwnedFollowingTransaction>
                    <value>235557</value>
                </sharesOwnedFollowingTransaction>
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                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
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        </nonDerivativeHolding>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
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                <value>2012-02-21</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
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                <transactionShares>
                    <value>942</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>38.90</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>173518</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Through trusts</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>59262</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Through family partnership</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes></footnotes>

    <remarks>This statement is being filed solely for informational purposes because of family relationships.  The filing of this statement is not an admission that the reporting person and any other person or persons constitute a &quot;group&quot; for purposes of Section 13(d)(3) of the Securities Exchange Act of 1934 or Rule 13d-5 thereunder or for any other purpose and the reporting person disclaims beneficial ownership of any shares other than those reported herein.</remarks>

    <ownerSignature>
        <signatureName>/s/ Daniel R. Tisch</signatureName>
        <signatureDate>2012-03-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
