FIRST SUPPLEMENTAL INDENTURE

Exhibit 4.1

FIRST SUPPLEMENTAL INDENTURE

By and Among

ExpressJet Holdings, Inc.

as Issuer,

ExpressJet Airlines, Inc.,

as Guarantor,

and

The Bank of New York Mellon Trust Company, N.A.,

as Trustee

Dated as of

July 30, 2008

A SUPPLEMENTAL INDENTURE

REGARDING

4.25% Convertible Notes due 2023

FIRST SUPPLEMENTAL INDENTURE

FIRST SUPPLEMENTAL INDENTURE dated as of July 30, 2008, among ExpressJet Holdings, Inc., a Delaware corporation (the “ Company ”), ExpressJet Airlines, Inc., a Delaware corporation (the “ Guarantor ”), and The Bank of New York Mellon Trust Company, N.A. (as successor in interest to Bank One, N.A.), as trustee (the “ Trustee ”);

WHEREAS, the Company and the Guarantor have heretofore executed and delivered to Bank One, N.A., as predecessor in interest to the Trustee, an indenture, dated as of August 4, 2003 (the “ Indenture ”), to provide for the issuance of the Company’s 4.25% Convertible Notes due 2023 (the “ Securities ”); and

WHEREAS, Section 9.01 of the Indenture provides, among other things, that the Company and the Trustee may amend the Indenture or the Securities without the consent of any Securityholder (as defined in the Indenture) to add to the Company’s or the Guarantor’s covenants for the benefit of the Securityholders, to add any additional Events of Defaults (as defined in the Indenture) or to provide security for the Securities; and

WHEREAS, the Company desires to amend the Indenture and the Securities as permitted by Section 9.01; and

WHEREAS, all action on the part of the Company necessary to authorize its execution, delivery and performance of the Indenture, as supplemented by this First Supplemental Indenture, has been duly taken; and

WHEREAS, the Company desires and has requested the Guarantor and the Trustee to join in the execution and delivery of this First Supplemental Indenture for the purpose of amending the Indenture and the Securities;

NOW THEREFORE, in consideration of the premises and for other good and valuable consideration, it is mutually covenanted and agreed for the equal and ratable benefit of all Securityholders as follows:

ARTICLE ONE

DEFINITIONS, ETC.

Section 1.1 Definitions . Each capitalized term that is used herein and is defined in the Indenture shall have the meaning specified in the Indenture unless such term is otherwise defined herein, in which case such term shall have the meaning specified herein.

Section 1.2 Conflict with Indenture . To the extent that any of the terms set forth in this First Supplemental Indenture shall conflict with any of the terms of the Indenture or the Securities, the terms of this First Supplemental Indenture shall be controlling.

ARTICLE TWO

AMENDMENTS TO INDENTURE

Section 2.1 Additional Covenants . Article IV of the Indenture is hereby amended by adding the following new Sections 4.08 and 4.09 to read as follows:

“SECTION 4.08. Payment of Additional Interest . Effective from and after the Effective Time, and notwithstanding anything to the contrary in this Indenture, in any Security or in the form of the Notes as set forth on Exhibit A-1, the Company promises to pay additional interest on the Principal Amount of the Securities at a rate of 7.00% per year from the Effective Time. During such period, the Company will pay such additional interest semiannually in arrears on each Interest Payment Date, commencing on February 1, 2009, and otherwise in accordance with the provisions of the Indenture and the Securities relating to the payment of interest. Without limiting the generality of the foregoing, such additional interest shall constitute “interest” for purposes of Section 6.01(1) of the Indenture.

SECTION 4.09. Additional Repurchase Date . Effective from and after the Effective Time, the date August 1, 2011 shall also be a “Repurchase Date” in addition to the dates set forth in Section 3.08.”

Section 2.2 Conforming Amendments Regarding Additional Covenants .

“, and additional interest on the Principal Amount of the Securities at a rate per annum of 7.00% per year from the Effective Time.”

Section 2.3 Title Change . The series of Securities previously designated as the “4.25% Convertible Notes due 2023” shall be designated as the “11.25% Convertible Secured Notes due 2023.”

Section 2.4 Additional Article . The Indenture is hereby amended by adding an additional new Article to be designated “ARTICLE XIV COLLATERAL AND SECURITY” and to read as follows:

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“ARTICLE XIV

COLLATERAL AND SECURITY”

SECTION 14.01. Security .

(a) From and after the Effective Time, the payment of the Securities, when due, and the performance of all other obligations of the Company and Guarantor under the Securities, this Indenture the Guarantee, and the Security Documents are secured by Liens upon the Guarantor’s rights in the Collateral.

(b) The Company shall, and shall cause the Guarantor to, do or cause to be done, at the sole expense of the Company and/or the Guarantor, all acts and things which may be required, or that the Collateral Agent from time to time may reasonably request, to assure and confirm that the Collateral Agent holds, for the benefit of the Holders of Securities, duly created, enforceable and perfected Liens upon the Collateral as contemplated by this Indenture and the Security Documents, so as to render the same available for the security and benefit of this Indenture and of the Securities and the Guarantee, according to the intent and purposes hereof expressed, subject in each case to any express provisions of any Security Documents. The Company shall take, or shall cause the Guarantor to take, upon request of the Trustee or Collateral Agent, any an all actions reasonably to create and maintain, as security for the obligations of the Company and Guarantor under this Indenture, the Guarantee and the Security Documents, a valid and enforceable perfected first priority Lien (subject to Permitted Liens) in and on the Collateral, in favor of the Collateral Agent and the Trustee, as the case may be, for the benefit of the Securityholders, which Lien is superior to and prior to the rights of all third Persons and subject to no other Liens, except Permitted Liens.

SECTION 14.02. Collateral Agent and Security Agreement .

(a) The Company and the Guarantor will enter into the Security Agreement with the Collateral Agent which sets forth the terms on which the Collateral Agent receives, holds, administers, maintains, enforces and distributes the proceeds of all Liens upon any Collateral at any time delivered to it, in trust for the benefit of the present and future Holders of the Securities.

(b) The Collateral Agent is authorized and empowered to appoint one or more co-Collateral Agents as it deems necessary or appropriate. Neither the Collateral Agent nor the Trustee shall not be responsible for any misconduct or negligence of any such co-Collateral Agent appointed with due care.

(c) Neither the Trustee nor the Collateral Agent nor any of their respective officers, directors, employees, attorneys or agents shall be responsible or liable for the existence, genuineness, value or protection of any Collateral, for the legality, enforceability, effectiveness or sufficiency of the Security Documents, for the creation, perfection, priority, sufficiency or protection of any Lien, or for any defect or deficiency as to any such matters, or for any failure to demand, collect, foreclose or realize upon or otherwise enforce any of the Liens or Security Documents or any delay in doing so.

(d) The Company appoints The Bank of New York Mellon as the initial Collateral Agent. The duties, rights, powers, and immunities of the Collateral Agent are

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contained in the Security Agreement to which reference is hereby made. No implied The Collateral Agent undertakes to perform such duties, and only such duties as are expressly herein and in the Security Agreement, and no implied covenants or obligations shall be read into this Indenture or the Security Agreement against the Collateral Agent.

SECTION 14.03. Release of Security Interests .

(a) In accordance with the provisions of the Security Agreement or as provided hereby, the Collateral Agent’s Liens upon the Collateral will be released:

(1) Upon the Discharge Date;

(2) as to any or all Collateral at any time, if (A) written consent to the release of Collateral has been given by an Act of Required Holders and (B) such release has become effective in accordance with the terms of such consent; or

(3) in accordance with the provisions of Section 14.05 and the Security Documents as in effect at the time of such release.

(b) The Collateral Agent’s Liens upon Collateral will no longer secure the Securities and the right of the Holders to the benefits and proceeds of the Collateral Agent’s Liens on Collateral will terminate and be discharged:

(1) upon discharge of this Indenture as set forth under in Section 8.01 hereof; or

(2) upon payment of the Securities, in full in cash or Common Stock, and the payment and satisfaction of all other related obligations of the Company and the Guarantor under the Securities, this Indenture and the Security Documents that are outstanding, due and payable at the time the Securities are so paid in full.

(c) The Company will otherwise comply with the provisions of TIA §314(b). To the extent applicable, the Company will cause TIA §313(b), relating to reports, and TIA §314(d), relating to the release of property or securities or relating to the substitution therefor of any property or securities to be subjected to the Liens imposed hereby and by the Security Documents, to be complied with. Any certificate or opinion required by TIA §314(d) may be an Officer’s Certificate, except in cases where TIA §314(d) requires that such certificate or opinion be made by an independent Person, which Person will be an independent appraiser or other expert selected or approved by the Trustee with reasonable care. To the extent applicable, the Company will furnish to the Trustee, prior to each proposed release of Collateral pursuant to the terms hereof and the Security Documents (i) all documents required by TIA §314(d); and (ii) an Opinion of Counsel to the effect that such accompanying documents constitute all documents required by TIA §314(d).

SECTION 14.04. Recording and Opinions .

(a) The Company shall furnish to the Collateral Agent and the Trustee contemporaneously with the execution and delivery of this First Supplemental Indenture and

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promptly after the execution and delivery of any other instrument of further assurance or amendment, an Opinion of Counsel (i) stating that in the opinion of such counsel the Security Documents are effective to create a Lien in the Collateral to the extent that the Guarantor has rights in or the power to transfer such Collateral and creation of a Lien in such collateral is governed by Article 9 of the UCC; and (ii) stating that in the opinion of such counsel, all action has been taken with respect to the filing of financing statements as is necessary to perfect the Lien in that portion of the Collateral (x) in which the Company has rights or the power to transfer, (y) the creation and perfection of a Lien which is governed by Article 9 of the UCC and (z) in which a Lien can be perfected by filing a financing statement under the UCC. Such Opinion of Counsel shall also address matters pertaining to the recordation of the Collateral with the Federal Aviation Aircraft Registry and the registration of the Liens in the International Registry as the Trustee may reasonably request.

(b) The Company shall furnish to the Collateral Agent and the Trustee on February 1 of each year beginning with February 1, 2008, an Opinion of Counsel, as of such date, stating that all action has been taken with respect to the filing of financing statements, continuation statements and other registrations and recordings as is necessary for the Lien in that portion of the collateral subject to the Security Documents (x) in which the Company has rights or the power to transfer, (y) the creation and perfection of a Lien which is governed by Article 9 of the UCC, and (z) in which a Lien can be perfected by filing a financing statement under the UCC, to continue to be perfected (or stating, in the opinion of such counsel. that no such action is necessary to maintain the Liens created by the Security Documents and the perfection thereof). Such Opinion of Counsel shall also address matters pertaining to the recordation of the Collateral with the Federal Aviation Aircraft Registry and the registration of the Liens in the International Registry as the Trustee may reasonably request.

(c) The Company will otherwise comply with the provisions of TIA §314(b).

SECTION 14.05. Release of Collateral .

(a) Subject to subsections (b), (c) and (d) of this Section 14.05, Collateral may be released from the Liens and security interest cr