Harsin, 37, was the head coach at Arkansas State last season, leading the Red Wolves to a 7-5 record, a tie for first in the Sun Belt Conference and a berth in the GoDaddy Bowl.
He was on the Boise State staff from 2001-2010 and spent two seasons as the co-offensive coordinator and quarterbacks coach at Texas.
"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," Athletic Director Mark Coyle said in a statement.
"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 replaces Chris Petersen, who left Boise State to become head coach at Washington. Harsin was an assistant to Petersen from 2006-10 when the Broncos went 61-5.
"One of the hardest decisions we ever made was leaving Boise," Harsin said. "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."
Harsin, a native of Boise, was a walk-on to the Boise State football team and was the back-up quarterback from 1995-99.
His leaving Arkansas State has the Red Wolves searching for a new head coach for the fifth time in five seasons.