On March 30, 1999, Crean was named head coach at Marquette University, beating out a number of candidates. While he was the coach at Marquette, the program averaged 20 wins a year, won a conference championship, and made six postseason appearances, including the 2003 NCAA Final Four, the program's third appearance all-time and first since 1977.

Crean was hired on April 1, 2008 as head coach of the Hoosiers and looks to bring his success from Milwaukee to Bloomington.

In 2012 ESPN.com named him National Coach of the Year and Sporting News named him the Big Ten Coach of the Year.