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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2015-12-11</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001635650</issuerCik>
        <issuerName>Green Plains Partners LP</issuerName>
        <issuerTradingSymbol>GPP</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001592476</rptOwnerCik>
            <rptOwnerName>Tourbillon Capital Partners, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>444 MADISON AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>26TH FLOOR</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>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Units representing limited partner interests</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2349708</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Tourbillon Global Master Fund, Ltd</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Units representing limited partner interests</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>12758</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Tourbillon Global Long Alpha Fund, LLC</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Notional Principal Amount Derivative Agreement</value>
                <footnoteId id="F1"/>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2015-12-11</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>1</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>14.2982</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-09-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Units representing limited partner interest</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Tourbillon Global Long Alpha Fund, LLC</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Notional Principal Amount Derivative Agreement</value>
                <footnoteId id="F1"/>
                <footnoteId id="F5"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F5"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2015-12-11</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>1</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>14.2982</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-07-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Units representing limited partner interest</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>16800</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F6"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Tourbillon Global Long Alpha Fund, Ltd</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Notional Principal Amount Derivative Agreement</value>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2015-12-14</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>1</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>14.3783</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-09-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Units representing limited partner interest</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>20000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F7"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Tourbillon Global Master Fund, Ltd</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Notional Principal Amount Derivative Agreement</value>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2015-12-15</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>1</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>14.3821</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-09-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Units representing limited partner interest</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>20000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F7"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Tourbillon Global Master Fund, Ltd</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This Form 4 is filed jointly by Tourbillon Capital Partners, L.P. (&quot;Tourbillon&quot;) and Jason H. Karp (together, the &quot;Reporting Persons&quot;). Each of the Reporting Persons may be deemed to be a member of a Section 13(d) group that may be deemed to collectively beneficially own more than 10% of the Issuer's outstanding Common Units. Each of the Reporting Persons disclaims beneficial ownership of the Common Units reported herein except to the extent of his or its pecuniary interest therein.</footnote>
        <footnote id="F2">Securities held for the account of Tourbillon Global Master Fund, Ltd (&quot;Global Master Fund&quot;). Each of Tourbillon, as the Investment Manager of Global Master Fund, and Jason H. Karp, as the Chief Executive Officer of Tourbillon, may be deemed to beneficially own the securities held for the account of Global Master Fund.</footnote>
        <footnote id="F3">Securities held for the account of Tourbillon Global Long Alpha Fund, LLC (&quot;Global Alpha Fund&quot;). Each of Tourbillon, as the Investment Manager of Global Alpha Fund, and Jason H. Karp, as the Chief Executive Officer of Tourbillon, may be deemed to beneficially own the securities held for the account of Global Alpha Fund.</footnote>
        <footnote id="F4">Notional principal amount derivative agreement (the &quot;Derivative Agreement&quot;) in the form of cash settled swaps entered into by Global Alpha Fund. The Derivative Agreement provides Global Alpha Fund with economic results that are comparable to the economic results of ownership payable on the settlement date applicable to the expiration or earlier termination of such Derivative Agreement, but does not provide it with the power to vote or direct the voting or dispose of or direct the disposition of the Common Units that are the subject of the Derivative Agreement (such securities, the &quot;Global Alpha Fund Subject Securities&quot;). Global Alpha Fund disclaims beneficial ownership in the Global Alpha Fund Subject Securities. The counterparty to the Derivative Agreement is an unaffiliated third party financial institution.</footnote>
        <footnote id="F5">Derivative Agreement in the form of cash settled swaps entered into by Tourbillon Global Long Alpha Fund, Ltd (&quot;Global Alpha Offshore Fund&quot;). The Derivative Agreement provides Global Alpha Offshore Fund with economic results that are comparable to the economic results of ownership payable on the settlement date applicable to the expiration or earlier termination of such Derivative Agreement, but does not provide it with the power to vote or direct the voting or dispose of or direct the disposition of the Common Units that are the subject of the Derivative Agreement (such securities, the &quot;Global Alpha Offshore Fund Subject Securities&quot;). Global Alpha Offshore Fund disclaims beneficial ownership in the Global Alpha Offshore Fund Subject Securities. The counterparty to the Derivative Agreement is an unaffiliated third party financial institution.</footnote>
        <footnote id="F6">Securities held for the account of Global Alpha Offshore Fund. Each of Tourbillon, as the Investment Manager of Global Alpha Offshore Fund, and Jason H. Karp, as the Chief Executive Officer of Tourbillon, may be deemed to beneficially own the securities held for the account of Global Alpha Offshore Fund.</footnote>
        <footnote id="F7">Derivative Agreement in the form of cash settled swaps entered into by Global Master Fund. The Derivative Agreement provides Global Master Fund with economic results that are comparable to the economic results of ownership payable on the settlement date applicable to the expiration or earlier termination of such Derivative Agreement, but does not provide it with the power to vote or direct the voting or dispose of or direct the disposition of the Common Units that are the subject of the Derivative Agreement (such securities, the &quot;Global Master Fund Subject Securities&quot;). Global Master Fund disclaims beneficial ownership in the Global Master Fund Subject Securities. The counterparty to the Derivative Agreement is an unaffiliated third party financial institution.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Brian A. Kessler, Chief Financial Officer of Tourbillon Capital Partners, L.P.</signatureName>
        <signatureDate>2015-12-15</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Jason H. Karp</signatureName>
        <signatureDate>2015-12-15</signatureDate>
    </ownerSignature>
</ownershipDocument>
