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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2011-06-06</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001368265</issuerCik>
        <issuerName>Clean Energy Fuels Corp.</issuerName>
        <issuerTradingSymbol>CLNE</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000898680</rptOwnerCik>
            <rptOwnerName>PICKENS BOONE</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLEAN ENERGY FUELS CORP.</rptOwnerStreet1>
            <rptOwnerStreet2>3020 OLD RANCH PARKWAY #400</rptOwnerStreet2>
            <rptOwnerCity>SEAL BEACH</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>90740</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2011-06-06</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>15000000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-12-28</value>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>15000000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2011-06-06</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>15000000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-12-28</value>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>15000000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>15000000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The two reported transactions involve an amendment of the warrant, resulting in the deemed cancellation of the &quot;old&quot; warrant and the grant of a replacement warrant.  The warrant was originally granted on December 28, 2006.</footnote>
        <footnote id="F2">Immediately.</footnote>
        <footnote id="F3">Pursant to the warrant amendment, if the Reporting Person exercises a portion of the warrant prior to December 28, 2011, the Issuer will extend the exercise period of the warrant to an identical number of shares for a length of time whereby the non-cash financial gain that the Issuer recognizes due to the early exercise period becomes identical to the non-cash financial charge the Issuer recongizes with respect to such extension.</footnote>
        <footnote id="F4">The warrant was issued to the Reporting Person in exchange for the cancellation of all amounts owed to him by the Issuer under a revolving line of credit.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Richard R. Wheeler, Attorney-in-Fact</signatureName>
        <signatureDate>2011-06-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
