On December 13, 2008, Auburn University hired Chizik to succeed former head coach Tommy Tuberville, who resigned from the position after finishing 5–7 in the 2008 season.
Auburn athletic director Jay Jacobs released a statement that said: "I know that we have found the right fit for Auburn.
Gene's body of work during his 23 years in this profession is remarkable.
He has a strong knowledge of this athletics program, this university and the community, and he knows how to be successful in the Southeastern Conference.
He is a high-energy coach that is an outstanding motivator and demands a tough, physical style of football."

Chizik first retained James Willis to continue coaching linebackers.
 However, less than one month later, Willis left Auburn to coach for the University of Alabama.
 Ted Roof would eventually replace Willis and serve as Auburn's linebacker coach and defensive coordinator.
 Roof had previously been the defensive coordinator at Minnesota before coming to Auburn.
Chizik hired Gus Malzahn as his offensive coordinator.
 Malzahn enjoyed the nation's top offense at Tulsa the previous two seasons.
He subsequently hired Curtis Luper and Trooper Taylor, both of whom were coaching at Oklahoma State, to coach running backs and wide receivers.
Chizik also brought Jay Boulware from his ISU staff to be the special teams coordinator and hired former Auburn player Tracy Rocker away from Arkansas to coach the defensive line.
The final hire was UNC linebackers coach Tommy Thigpen as safeties coach.

Chizik's incentive-laden contract at Auburn was for five years with a salary of approximately $1.9 million per year, an $800,000 increase from his Iowa State contract.
Iowa State was paid $750,000 by Chizik to be released from his contract which was paid by a loan from Auburn that was forgiven $150,000 for every year Chizik coaches, and would have been paid off entirely if he reached the end of the five-year deal.
For the BCS Championship winning 2010 season, Chizik earned a base salary of $2.1 million plus bonuses worth an additional $1.1 million, including $500,000 for 13 wins, an SEC title, a BCS bowl appearance and winning the AP SEC Coach of the Year and an additional $600,000 for winning the BCS Championship Game.

In his first year, Chizik led the Tigers to the 2010 Outback Bowl, a fairly quick turnaround for a team that went 5–7 the year before.
 The next year, he led the team to a 14–0 record and the BCS National Championship—the first undisputed national championship in school history.
 With the loss of several players from that team who opted to go pro, Chizik's third team slipped to 8–5.
The 2012 season was the first season that Chizik did not have Gus Malzahn on staff; Malzahn had accepted a Head Coaching Position at Arkansas State following the 2011 season.
The 2012 season was extremely disappointing as the team finished 3–9 and was outscored 150–21 in its final three SEC games—including a 49–0 loss to Alabama in the Iron Bowl.
Overall, Auburn went 33–19 during Chizik's tenure as head football coach.

Chizik was released after four seasons, and his termination cost Auburn $11.09 million.
Chizik got $7.5 million based on his December 1 contractual buyout amount and assistant coaches got the remainder.
On December 13, 2008, Auburn University hired Chizik to succeed former head coach Tommy Tuberville, who resigned from the position after finishing 5–7 in the 2008 season. Auburn athletic director Jay Jacobs released a statement that said: "I know that we have found the right fit for Auburn. Gene's body of work during his 23 years in this profession is remarkable. He has a strong knowledge of this athletics program, this university and the community, and he knows how to be successful in the Southeastern Conference. He is a high-energy coach that is an outstanding motivator and demands a tough, physical style of football."
Chizik first retained James Willis to continue coaching linebackers.  However, less than one month later, Willis left Auburn to coach for the University of Alabama.  Ted Roof would eventually replace Willis and serve as Auburn's linebacker coach and defensive coordinator.  Roof had previously been the defensive coordinator at Minnesota before coming to Auburn. Chizik hired Gus Malzahn as his offensive coordinator.  Malzahn enjoyed the nation's top offense at Tulsa the previous two seasons. He subsequently hired Curtis Luper and Trooper Taylor, both of whom were coaching at Oklahoma State, to coach running backs and wide receivers. Chizik also brought Jay Boulware from his ISU staff to be the special teams coordinator and hired former Auburn player Tracy Rocker away from Arkansas to coach the defensive line. The final hire was UNC linebackers coach Tommy Thigpen as safeties coach.
Chizik's incentive-laden contract at Auburn was for five years with a salary of approximately $1.9 million per year, an $800,000 increase from his Iowa State contract. Iowa State was paid $750,000 by Chizik to be released from his contract which was paid by a loan from Auburn that was forgiven $150,000 for every year Chizik coaches, and would have been paid off entirely if he reached the end of the five-year deal. For the BCS Championship winning 2010 season, Chizik earned a base salary of $2.1 million plus bonuses worth an additional $1.1 million, including $500,000 for 13 wins, an SEC title, a BCS bowl appearance and winning the AP SEC Coach of the Year and an additional $600,000 for winning the BCS Championship Game.
In his first year, Chizik led the Tigers to the 2010 Outback Bowl, a fairly quick turnaround for a team that went 5–7 the year before.  The next year, he led the team to a 14–0 record and the BCS National Championship—the first undisputed national championship in school history.  With the loss of several players from that team who opted to go pro, Chizik's third team slipped to 8–5. The 2012 season was the first season that Chizik did not have Gus Malzahn on staff; Malzahn had accepted a Head Coaching Position at Arkansas State following the 2011 season. The 2012 season was extremely disappointing as the team finished 3–9 and was outscored 150–21 in its final three SEC games—including a 49–0 loss to Alabama in the Iron Bowl. Overall, Auburn went 33–19 during Chizik's tenure as head football coach. 
Chizik was released after four seasons, and his termination cost Auburn $11.09 million. Chizik got $7.5 million based on his December 1 contractual buyout amount and assistant coaches got the remainder.
Gene Chizik