Linder, an assistant coach with the Broncos the last three seasons, fills the role vacated by Dave Wojcik, who was named head coach at San Jose State, March 29.
"Jeff has played a major role in building this program," Rice said. "He possesses high-level knowledge of the game of basketball, and has the ability to identify and develop talent. Jeff earned this promotion, and we are grateful to have him as a member of our staff."
Linder helped lead the Broncos to the NCAA Tournament this past season, the first at-large selection in school history. Boise State went 21-11 in 2012-13, the Broncos' second 20-win campaign in Linder's three seasons with the team.
He previously served as associate head coach at San Francisco in 2009-10 before joining the Broncos the following season.