EXHIBIT 10.1

Exhibit 10.1

Execution Version

**SECOND AMENDMENT TO **
***DRAW DOWN NOTE PURCHASE AND CONTINUING COVENANT AGREEMENT ***

THIS SECOND AMENDMENT TO DRAW DOWN NOTE PURCHASE AND CONTINUING COVENANT AGREEMENT (this “Amendment”) is dated June 29, 2026 (the “Second Amendment Effective Date”), and is made by and among SKY HARBOUR CAPITAL II LLC, a Delaware limited liability company (“SH Capital II LLC”), BDL HANGARS LLC, a Delaware limited liability company (“BDL Hangars”), CLOUDNINE AT CAMARILLO LIMITED PARTNERSHIP, a California limited partnership (“CloudNine at Camarillo”), and SLC DEVELOPMENT LLC, a Delaware limited liability company (“SLC Development” and, together with SH Capital II LLC, BDL Hangars and CloudNine at Camarillo, the “Borrowers”), as the borrowers party hereto as of the Second Amendment Effective Date, the lenders party hereto (the “Lenders”), and JPMORGAN CHASE BANK, N.A., as Administrative Agent (the “Administrative Agent”).

RECITALS

WHEREAS, the Borrowers, the Lenders and the Administrative Agent are parties to that certain Draw Down Note Purchase and Continuing Covenant Agreement dated as of September 4, 2025 (the “Original Credit Agreement”), as previously amended by the First Amendment to Draw Down Note Purchase and Continuing Covenant Agreement, dated January 8, 2026 (the “First Amendment” and, together with the Original Credit Agreement, the “Credit Agreement”); and

WHEREAS, SH Capital II LLC has requested that the Lenders and the Administrative Agent amend certain provisions of the Credit Agreement, and the Lenders and the Administrative Agent are willing to make such amendments, in each case, in the manner and on the terms and conditions set forth herein.

NOW, THEREFORE, in consideration of the above Recitals and the mutual covenants herein contained and for other valuable consideration, the receipt and sufficiency of which are hereby acknowledged, and intending to be legally bound hereby, the parties hereto do hereby agree as follows:

“2026 PABs” means the Public Finance Authority Revenue Bonds (Sky Harbour Capital III LLC Aviation Facilities Project), Series 2026, originally issued in the principal amount of $150,000,000.

“Equity Replenishment Amount” has the meaning assigned to it in Section 5.21(a).

“Equity Replenishment Conditions” has the meaning assigned to it in Section 5.21(c).

“Equity Replenishment Period” has the meaning assigned to it in Section 5.21(a).

“OPF II Borrowing” has the meaning assigned to it in Section 2.03A.

“OPF II Project” has the meaning assigned to it in the First Amendment to Loan and Security Agreement dated June 29, 2026, by and among SH Capital II LLC, the other Borrowers, the Administrative Agent and the Issuer.

“OPF II Project Costs” has the meaning assigned to it in Section 2.03A(c).

“OPF II Project Owner” means Sky Harbour Opa Locka Airport, LLC, a Delaware limited liability company.

“OPF II Transmittal and Reimbursement” has the meaning assigned to it in Section 2.03A(e).

“SJC Hangars” has the meaning assigned to it in Section 6.17.

“SJC Project” means the Sky Harbour private hangar campus and related improvements, easements, leasehold interests, contracts, permits, equipment, fixtures and other tangible and intangible assets located at or relating to Norman Y. Mineta San José International Airport, San Jose, California, in each case owned, leased, ground-leased, licensed, held or used by the SJC Project Entities.

“SJC Project Entities” has the meaning assigned to it in Section 6.17.

“SKYH National” has the meaning assigned to it in Section 6.17.

“SECTION 2.03A. Special Borrowing Request. Notwithstanding any provision of Section 2.03 or any other provision of this Agreement to the contrary, on or before December 31, 2026, the Borrower Representative may request, and the Lenders shall make, a Borrowing for the purpose of financing or reimbursing the costs of the OPF II Project in an aggregate principal amount not to exceed

$20,000,000 (the “OPF II Borrowing”), provided that the following conditions have been satisfied on or prior to the date of such Borrowing:

For the avoidance of doubt, except as otherwise set forth in this Section 2.03A, the provisions of Sections 2.04 and 2.05 shall not apply to the OPF II Borrowing.

The Administrative Agent and the Lenders hereby agree that, for purposes of this Agreement, (x) the OPF II Project Owner is not a Borrower, (y) the OPF II Project is not and will not be an Eligible Project, is not and will not be an Approved Eligible Project, and is not will not be included in the Borrowing Base, and (z) the OPF II Transmittal and Reimbursement is expressly permitted hereby, notwithstanding any other provision of this Agreement to the contrary (including, without limitation, Sections 5.08, 6.05, 6.07 and 6.17 hereof).

SECTION 5.21. Equity Replenishment.

For the avoidance of doubt the Equity Replenishment Amount shall not be taken into account in determining the Minimum Equity Requirement for any Approved Eligible Project.

SECTION 6.17. SJC Project Negative Pledge. Until the Equity Replenishment Conditions are satisfied, the Borrower Representative shall cause Sky Harbour National Holdings LLC (“SKYH National”), SJC Hangars LLC (“SJC Hangars”) and each other direct or indirect subsidiary of SKYH National that owns or leases all or any portion of the SJC Project (together with SJC Hangars, the “SJC Project Entities”) not to, directly or indirectly:

The Borrowers shall (i) cause SKYH National to take all actions reasonably necessary to ensure that the SJC Project Entities comply with this Section 6.17, and

(ii) deliver to the Administrative Agent, promptly upon request, such certificates, lien searches, organizational chart updates and other evidence of compliance with this Section 6.17 as the Administrative Agent may reasonably require.

(d)  any Borrower shall fail to observe or perform any covenant, condition or agreement contained in Section 5.02, 5.03 (with respect to the existence of any Borrower), 5.08, 5.12, 5.13, 5.16, 5.17 or 5.21 or in Article VI;