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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2007-09-11</periodOfReport>

    <dateOfOriginalSubmission>2007-09-21</dateOfOriginalSubmission>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001361709</issuerCik>
        <issuerName>Susser Holdings CORP</issuerName>
        <issuerTradingSymbol>SUSS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001412601</rptOwnerCik>
            <rptOwnerName>Engel David P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SUSSER HOLDINGS CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>4525 AYERS STREET</rptOwnerStreet2>
            <rptOwnerCity>CORPUS CHRISTI</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78415</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, par value $0.01 per share</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5600</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, par value $0.01 per share</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>57467</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">This amendment on Form 3/A to the Form 3 originally filed on September 21, 2007 (the &quot;Original Form 3&quot;) is made solely to correct the shares of Common Stock in Table 1. Due to an inadvertent error, the amount of securities beneficially owned directly was transposed with the amount of securities beneficially owned indirectly on the Original Form 3 and subsequent filings made with the SEC pursuant to Section 16 of the Securities Exchange Act of 1934, as amended.</footnote>
        <footnote id="F2">Shares of stock owned by Engel Investments, Ltd. The Reporting Person serves as the president of the general partner of Engel Investments, Ltd.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ E.V. Bonner, Jr., Attorney-in-fact</signatureName>
        <signatureDate>2013-03-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
