Exhibit 10.1

ELEVENTH SUPPLEMENTAL INDENTURE

Eleventh Supplemental Indenture (this “Supplemental Indenture”), dated as of November 17, 2020, by and among Navios
Maritime Acquisition Corporation, a Marshall Islands corporation (the “Company”) and Navios Acquisition Finance (US) Inc., a Delaware corporation (“Navios Finance” and together with the Company, the
“Co-Issuers”), the guarantors party hereto (the “Guarantors”) and Wilmington Trust, National Association, in its capacity as trustee (the “Successor Trustee”) and as collateral trustee (the
“Successor Collateral Trustee”) under the Indenture referenced below.

WITNESSETH:

WHEREAS, the Co-Issuers, the Guarantors party thereto and Wells Fargo Bank, National Association, a national banking association, as
trustee (in such capacity, the “Prior Trustee”) and as collateral trustee (in such capacity, the “Prior Collateral Trustee”) entered into that certain Indenture dated as of November 13, 2013 (as amended,
modified or supplemented from time to time, the “Indenture”), providing for the issuance of the Co-Issuers’ 8.125% First Priority Ship Mortgage Notes due 2021 (the “Notes”);

WHEREAS, Sections 7.08 and 11.17 of the Indenture provide that the Trustee and the Collateral Trustee under the Indenture and the
Security Documents may resign as Trustee and as Collateral Trustee under the Indenture and the Security Documents, respectively, in accordance with the terms of the Indenture, and a successor Trustee and successor Collateral Trustee may be appointed
as Trustee and Collateral Trustee under the Indenture and the Security Documents, respectively, pursuant to which such appointment, each of the successor Trustee and successor Collateral Trustee shall accept such appointment and all of the rights,
powers, duties and obligations of the prior Trustee and the prior Collateral Trustee under the Indenture and the Security Documents, respectively.

WHEREAS, pursuant to the Successor Trustee Agreement, dated as of November 17, 2020 (the “Successor Trustee
Agreement’
), by and among the Co-Issuers, the Prior Trustee, the Prior Collateral Trustee, the Successor Trustee and the Successor Collateral Trustee, the Prior Trustee and the Prior Collateral Trustee have resigned as Trustee and
Collateral Trustee under the Indenture and the Security Documents, respectively, in accordance with the terms of the Indenture, and the Successor Trustee and the Successor Collateral Trustee have been appointed as the successor Trustee and the
successor Collateral Trustee under the Indenture and the Security Documents, respectively, pursuant to which such appointment, each of the Successor Trustee and the Successor Collateral Trustee has accepted its appointment and all of the rights,
powers and obligations of the Prior Trustee or the Prior Collateral Trustee under the Indenture and the Security Documents, as applicable;

WHEREAS, Section 9.01(8) of the Indenture provides that the Indenture and the Security Documents may be amended or supplemented by
the Co-Issuers, the Guarantors, the Trustee and the Collateral Trustee, as applicable, in accordance with the terms of the Indenture, without the consent of any Holder to evidence and provide for the acceptance of appointment under the Indenture by
a successor Trustee or Collateral Trustee;



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