He became head coach in 1992 and in 1994 Hughes reached the state championship game with an upset of Pine Bluff Dollarway.

Hughes fell just short in the title game, losing to Lonoke High School on an interception in the final minute.

Malzahn's success at Hughes and his wide-open attack landed him a head coaching position at Shiloh Christian School in 1996.

Included on the championship team were prize recruits Mitch Mustain, Ben Cleveland, Andrew Norman, and Damian Williams who all eventually joined Malzahn at the University of Arkansas.

Offensive tackle Bartley Webb decided to leave the state to play for the University of Notre Dame.

In January 2007, Malzahn received an offer from the University of Tulsa and his friend, new head coach Todd Graham.

Shortly after the departure of Coach Graham and Malzahn, both Arkansas star quarterback Mitch Mustain and receiver Damien Williams decided to transfer to the University of Southern California.

[18] Tulsa quarterbacks David Johnson and G. J. Kinne finished third in the nation in passing efficiency, behind only Oklahoma and Texas.

[19] Malzahn was named the offensive coordinator at Auburn University by first year head coach Gene Chizik on December 28, 2008.

Head coach Gene Chizik had stressed prior to the season that he intended to focus on the run game which showed great improvement as well; the rushing offense finished the season ranked 13th in the nation with 212 yards per game[25] after being ranked 69th prior to the new coaching staff's arrival.

[28] Senior quarterback Chris Todd set a single-season touchdown record at Auburn and finished the season with a passer rating of 145.73, ranking him 18th in the nation.

[31] Malzahn's offense, led by eventual Heisman Trophy winner Newton at quarterback, helped Auburn achieve an undefeated record, a No.

[33] Malzahn resigned as the head coach at UCF on November 30, 2024, to become the new offensive coordinator at Florida State.

[34] On December 13, 2011, Malzahn left Auburn to accept the position of head football coach at Arkansas State University.

[41] On December 4, 2012, Malzahn was announced to replace Gene Chizik as the head coach of Auburn University shortly after winning the Sun Belt Conference Championship.

On November 16, 2013, with the Tigers down by 1 against Georgia facing 4th-and-18 and 36 seconds left in the game, Malzahn called the play "Little Rock" for Marshall which would become known as "The Prayer at Jordan–Hare".

Marshall hit Ricardo Louis on a tipped 73-yard Hail Mary pass to give Auburn the victory.

Two weeks later, in the Iron Bowl against Alabama, Malzahn's Tigers avenged two consecutive blowout losses to the Tide with a dramatic 34–28 win, clinched on an epic 109-yard return of a missed field goal for the game-winning touchdown as time expired, nicknamed the "Kick Six".

Heisman Trophy winner Jameis Winston stepped up in the fourth quarter and rallied the Seminoles to a victory, leading the way with 6-of-7 passing for 77 yards en route to the go-ahead scoring touchdown.

On December 10, fans voted him the recipient of the inaugural Premier Coach of College Football Award.

On December 23, it was announced that Malzahn had won the Associated Press National Coach of the Year, edging out Duke's David Cutcliffe, 33 votes to 17.

Despite the schedule and various team injuries, Malzahn managed to lead the Tigers to a New Year's Six Sugar Bowl appearance against Oklahoma.

[44][45] Kamryn Pettway led the SEC and ranked 11th in the nation in rushing yards per game, which made him a Doak Walker Award semifinalist (top running back in college football).

[53] On December 13, 2020, Malzahn was fired as head coach of Auburn at the conclusion of his eighth winning season.

[55] Malzahn reached fifth on Auburn's all-time wins list, behind Shug Jordan, Mike Donahue, Pat Dye and Tommy Tuberville.

[59] On February 15, 2021, Malzahn was named the head coach at UCF, reuniting him with former Arkansas State athletic director Terry Mohajir.

After an injury-plagued season, the starting lineup was missing 27 total starters or rotational players going into the bowl game.

Despite the team injuries, he led the Knights to a (29–17) victory over in-state rival Florida in the Gasparilla Bowl, finishing with a 9–4 overall record in his first season with UCF.

On November 30, 2024, following the (14-28) loss to Utah, Malzahn resigned from his job as head coach at UCF to become the offensive coordinator at FSU.

In January 2003, he published a book and instructional video titled Hurry Up No Huddle – An Offensive Philosophy (ISBN 9781585186549).