Exhibit 10.6

FIRST AMENDMENT TO SECURITY AGREEMENT

THIS FIRST AMENDMENT TO SECURITY AGREEMENT is entered into as of March 23, 2007
(this “Amendment”), by and between Great Lakes Aviation Ltd., as debtor (the
“Debtor”), and Raytheon Aircraft Credit Corporation (the “Secured Party”).

WITNESSETH:

WHEREAS, Debtor and Secured Party are parties to a Security Agreement dated as
of December 31, 2002 pursuant to which the Debtor granted to the Secured Party a
lien on substantially all of its assets (the “Security Agreement”; capitalized
terms used and not defined herein shall have the meanings ascribed thereto in
the Security Agreement);

WHEREAS, Debtor has entered into an Amended and Restated Restructuring Agreement
dated as of March 9, 2007 with the Secured Party (as amended and in effect from
time to time, the “2007 Restructuring Agreement”) whereby, among other things,
the Secured Party has agreed to restructure certain of its indebtedness owing to
RACC;

WHEREAS, the parties intend by this instrument to amend the Security Agreement
as of the date hereof to specifically reflect that the references in the
Security Agreement to the “Restructuring Agreement” are to the 2007
Restructuring Agreement;

NOW, THEREFORE, for good and valuable consideration, the receipt and sufficiency
of which is acknowledged, the parties hereto agree as follows:

 

1. The definition of the “Restructuring Agreement” in the Security Agreement is
hereby amended to mean the 2007 Restructuring Agreement, as it may be amended or
amended and restated and in effect from time to time.

 

2. Except as modified and supplemented hereby, the Security Agreement remains in
full force and effect and is hereby ratified and confirmed.

 

3. THIS AMENDMENT WAS MADE AND ENTERED INTO IN THE STATE OF KANSAS AND THE LAW
GOVERNING THIS TRANSACTION SHALL BE THAT OF THE STATE OF KANSAS AS IT MAY FROM
TIME TO TIME EXIST. THE PARTIES AGREE THAT ANY LEGAL PROCEEDING BASED UPON THE
PROVISIONS OF THIS AMENDMENT OR THE SECURITY AGREEMENT AS AMENDED HEREBY SHALL
BE BROUGHT EXCLUSIVELY IN EITHER THE UNITED STATES DISTRICT COURT FOR THE
DISTRICT OF KANSAS AT WICHITA, KANSAS, OR IN THE EIGHTEENTH JUDICIAL DISTRICT
COURT OF SEDGWICK COUNTY, KANSAS, TO THE EXCLUSION OF ALL OTHER COURTS AND
TRIBUNALS.

 

Security Agreement Amendment

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NOTWITHSTANDING THE ABOVE, IN THE EVENT AN “EVENT OF DEFAULT” SHOULD OCCUR, RACC
(AT ITS SOLE OPTION) MAY INSTITUTE A LEGAL PROCEEDING IN ANY JURISDICTION AS MAY
BE APPROPRIATE IN ORDER FOR RACC TO OBTAIN POSSESSION OF THE COLLATERAL. THE
PARTIES HEREBY CONSENT AND AGREE TO BE SUBJECT TO THE JURISDICTION OF THE
AFORESAID COURTS IN SUCH PROCEEDINGS. THE PARTIES EACH IRREVOCABLY WAIVES ANY
OBJECTION, INCLUDING ANY OBJECTION TO THE LAYING OF VENUE OR BASED ON THE
GROUNDS OF FORUM NON CONVENIENS, WHICH IT MAY NOW OR HEREAFTER HAVE TO THE
BRINGING OF ANY ACTION OR PROCEEDING IN SUCH JURISDICTION IN RESPECT OF THIS
AMENDMENT, THE SECURITY AGREEMENT AS AMENDED HEREBY OR OTHER DOCUMENT RELATED
THERETO. THE PARTIES EACH WAIVES PERSONAL SERVICE OF ANY SUMMONS, COMPLAINT OR
OTHER PROCESS, WHICH MAY BE MADE BY ANY OTHER MEANS PERMITTED BY THE LAW OF SUCH
APPLICABLE STATE.

 

4. ALL PARTIES TO THIS AMENDMENT HEREBY VOLUNTARILY, KNOWINGLY AND IRREVOCABLY
WAIVE ANY CONSTITUTIONAL OR OTHER RIGHT EACH MAY HAVE TO A TRIAL BY JURY IN THE
EVENT OF LITIGATION CONCERNING THIS AMENDMENT OR THE SECURITY AGREEMENT AS
AMENDED HEREBY.

 

5. This Amendment may be executed and delivered by the parties hereto in
separate counterparts, each of which when executed and delivered, shall be an
original, but all such counterparts shall together constitute but one and the
same instrument.

[Remainder of this page intentionally left blank.]

 

Security Agreement Amendment

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Executed as of this 23 day of March, 2007, at Wichita, Kansas.

 

GREAT LAKES AVIATION, LTD.   RAYTHEON AIRCRAFT CREDIT CORPORATION By:  

/s/ Michael Matthews

  By:  

/s/ Andrew Mathews

Name:   Michael Matthews   Name:   Andrew Mathews Title:   Chief Financial
Officer   Title:   President

 

Security Agreement Amendment