Before leaving for Texas in 2011, Harsin was an assistant at Boise State for 10 seasons, the last five as offensive coordinator and quarterbacks coach.

[3][4] Harsin got his start at Eastern Oregon University in La Grande, coaching running backs and quarterbacks in the 2000 season.

When Hawkins left BSU for Colorado, offensive coordinator Chris Petersen was promoted to head coach for the 2006 season.

During Harsin's tenure as offensive coordinator, Boise State posted a 61–5 (.924) record, which included two undefeated seasons and two Fiesta Bowl victories, over Oklahoma (2007) and TCU (2010).

[10] Harsin became the 29th head coach at Arkansas State University in Jonesboro on December 12, 2012, succeeding Gus Malzahn, who left for Auburn after just one season.

[11] Because Malzahn and his predecessor Hugh Freeze left after just one season in Jonesboro, Harsin's contract at Arkansas State included a $1.75 million buyout clause.

[16] In his first season at the helm, he led his team to a win at the Mountain West Championship against Fresno State 28–14, and earned a spot in the Fiesta Bowl against Arizona.

Harsin was hired on December 22, 2020, as the 27th head coach of the Auburn Tigers, taking over after the termination of Gus Malzahn.

[21][22][23] Despite the losing record, the season saw ranked victories over Arkansas and Ole Miss to go along with a narrow 24–22 4OT loss to #3 Alabama.

[30] In addition to the coordinatoring changeovers, 31 players left the program including starting quarterback Bo Nix who described his time under Harsin as "miserable".