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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2012-11-30</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001347815</issuerCik>
        <issuerName>Flagstone Reinsurance Holdings, S.A.</issuerName>
        <issuerTradingSymbol>FSR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001411821</rptOwnerCik>
            <rptOwnerName>WATSON PETER F</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSTONE REINSURANCE HOLDINGS, S.A.</rptOwnerStreet1>
            <rptOwnerStreet2>65 AVENUE DE LA GARE</rptOwnerStreet2>
            <rptOwnerCity>LUXEMBOURG</rptOwnerCity>
            <rptOwnerState>N4</rptOwnerState>
            <rptOwnerZipCode>L-1611</rptOwnerZipCode>
            <rptOwnerStateDescription>LUXEMBOURG</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted Share Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0</value>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2012-11-30</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>19151</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Shares</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>19151</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Each Restricted Share Unit (&quot;RSU&quot;) represents the right to receive, without payment to the Company, one newly issued, fully paid and non-assessable common share of the Company, subject to the terms and conditions of the RSU Plan and grant certificate evidencing each grant. In the discretion of the Compensation Committee, upon exercise, the RSU grant may alternatively be paid in cash, or partly in cash and partly in common shares.</footnote>
        <footnote id="F2">The RSUs, which were 100% vested on the date of grant, were converted pursuant to the Agreement and Plan of Merger, dated as of August 30, 2012 by and among the Company, Flagstone Reinsurance Holdings (Bermuda) Limited, Validus Holdings, Ltd. (&quot;Validus&quot;) and Validus UPS, Ltd. (the &quot;Merger Agreement&quot;) into the right to receive, for each RSU, (A) a cash payment of $2.00 plus the amount of cumulative dividends declared by the Company with respect to the common shares underlying such RSUs through the date on which the mergers contemplated by the Merger Agreement were consummated and (b) 0.1935 common shares of Validus (as of November 29, 2012, the closing price of common shares of Validus was $34.87 per share).</footnote>
        <footnote id="F3">The RSUs had no expiry date.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ William F. Fawcett, by power of attorney</signatureName>
        <signatureDate>2012-11-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
