Harsin will replace Chris Petersen, who left Boise State last week to become the coach at Washington. Harsin had previously worked as a Broncos assistant, serving as the team's offensive coordinator from 2006 to '10.
In a statement Boise State athletic director Mark Coyle said the program is excited to bring back a familiar face.
"We are extremely excited in our selection of Bryan Harsin as the next head football coach at Boise State," Coyle said. "Bryan is one of the top young head coaches in college football and we are thrilled to bring him back to Boise to lead the Bronco program. Bryan played a key role in the development of the football program as an assistant for 10 years at Boise State and we look forward to his leadership as we continue the ascension of Bronco football."
Harsin said a return to Boise State is a homecoming of sorts for his family.
"We're coming home," Harsin said. "Kes and I are thrilled about returning to Boise State, it's a special place built by special people. One of the hardest decisions we ever made was leaving Boise. We did that so I could become a better coach, so I could one day have the opportunity to return as head coach - that day has arrived.
"I appreciate the history and tradition of the Boise State program," Harsin continued. "I embrace that success but won't rest on it. We will build this program every day with a sense of urgency. I can't wait to get to work. Go Broncos!"
Arkansas State hired Harsin in December 2012 to replace Gus Malzahn, who spent just one season in Jonesboro before he accepted the Auburn job in December of last year. Harsin led the Red Wolves to a 7-5 (5-2 Sun Belt) record this season.
Harsin arrived at Arkansas State as one of the most respected assistants in the country, having been a member of the Boise State coaching staff for 10 season before moving on to Texas, where he was the Longhorns' co-offensive coordinator and quarterbacks coach in 2011 and '12. During Harsin's five seasons as the Broncos' offensive coordinator, Boise State ranked among the top five nationally in scoring four times and won 61 of 66 games.