Harsin replaces former Auburn coach Gus Malzahn, who was fired earlier this month after eight seasons at the school.
"I knew it would take a special opportunity to get me out of Boise and Auburn is exactly that, the chance to compete at the highest level for one of the greatest programs in college football," Harsin said in a statement.
"I have a tremendous amount of respect for the coaches and players in the Southeastern Conference, but am ready to help build a foundation at Auburn where we can consistently compete for championships. I want our program to make Auburn proud both on and off the field with consistent excellence."
The 44-year-old Harsin posted a 69-19 record and won three Mountain West titles in seven seasons at Boise State, his alma mater. According to ESPN, Harsin was one of the top targets for Auburn since the beginning of its coaching search.
"We are thrilled to welcome Coach Harsin to the Auburn family," Auburn athletic director Allen Greene said in a statement. "He's a proven winner whose record speaks for itself. Coach Harsin impressed me with his detailed plan to lead Auburn to consistently compete for championships in the Southeastern Conference."
Auburn fired Malzahn after a 6-4 record in the 2020 regular season. The move cost the school more than $21 million to buy out his contract.
Since reaching the national championship game in Malzahn's first season in 2013, the Tigers have lost at least four games in every season.
Auburn is scheduled to play No. 14 Northwestern in the Citrus Bowl on New Year's Day. Tigers defensive coordinator Kevin Steele is serving as the team's interim head coach for the game.