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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2013-04-01</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001159154</issuerCik>
        <issuerName>REPUBLIC AIRWAYS HOLDINGS INC</issuerName>
        <issuerTradingSymbol>RJET</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001518270</rptOwnerCik>
            <rptOwnerName>Dooley Timothy P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O REPUBLIC AIRWAYS HOLDINGS INC.</rptOwnerStreet1>
            <rptOwnerStreet2>8909 PURDUE ROAD, SUITE 300</rptOwnerStreet2>
            <rptOwnerCity>INDIANAPOLIS</rptOwnerCity>
            <rptOwnerState>IN</rptOwnerState>
            <rptOwnerZipCode>46268</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP, CFO, Treasurer, Secretary</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, $.001 par value</value>
            </securityTitle>
            <transactionDate>
                <value>2013-04-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>6666</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.86</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>80001</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These shares were sold pursuant to a written plan as specified in Rule 10b5-1 of the Securities Exchange Act of 1934.</footnote>
        <footnote id="F2">This number includes 80,001 restricted shares, of which 10,000 are vested, 10,000 vest in equal annual installments from June 22, 2013 and June 22, 2014, 6,667 vest on December 31, 2013, 33,334 vest in equal annual installments from March 30, 2014 to March 30, 2015, and 20,000 vest in equal annual installments from March 11, 2014 to March 11, 2016.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Timothy P. Dooley</signatureName>
        <signatureDate>2013-04-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
