Prior to that, he served as head coach at Marquette University (1999–2008), where his team reached the 2003 NCAA Final Four.

His guidance of the Indiana program to success from "unthinkable depths" was regarded as one of the most remarkable rebuilding projects in NCAA basketball history.

"[2] While a student at Central Michigan University, Crean was an assistant coach at Mount Pleasant High School for five seasons,[3] and at Alma College.

[2] Crean is married to Joani Harbaugh, whom he met while an assistant to Ralph Willard at Western Kentucky University (WKU) through a mutual friend, Ron Burns, at a gym where she was working as an aerobics instructor.

"[11] During this period Crean served at various times as recruiting coordinator and, for the last two seasons, associate head coach.

Michigan State later went on to honor Crean with a 2000 National Championship ring; even though he wasn't on the staff at the time, he'd helped recruit and develop many of the players on the title team.

[14] Crean's first recruiting class was considered by experts to be among the top twenty in the country, Marquette's first in a long time.

During his tenure there Crean recruited, developed and coached a number of skilled players that made significant contributions in both the NCAA and NBA, including Dwyane Wade, Dominic James, Steve Novak, Wesley Matthews, and Travis Diener.

Big East commissioner Mike Tranghese cited his friendship with Crean as contributing to the invitation, saying, "That, to me, was one of the great appeals, to get Tommy as well as Marquette into the league.

Between Crean's hiring and the start of the 2008–09 season, freshman Eric Gordon opted to leave early for the NBA and star forward DJ White graduated.

[19] As a result, Crean began with a roster consisting only of two walk-ons who had scored a combined 36 points in their careers.

"[20] With a depleted roster and reduced recruiting allure, Crean's first three seasons saw consecutive losing records of 6–25 (the worst in school history), 10–21, and 12–20.

For instance, at the first "Midnight Madness" festivities before his first season, Crean brought back "Martha the Mop Lady," the subject of a popular ad that opened Hoosier basketball games on WTTV for 30 years.

Starting with the 2010–11 season, video of the original ad was shown at home games after the National Anthem and right before tip off.

After defeating VCU in the Round of 32, the Hoosiers lost in the Sweet Sixteen to rival Kentucky, who would go on to win the national championship.

[22] Crean's guidance of the program to success from "unthinkable depths" was widely regarded as one of the most remarkable rebuilding projects in NCAA basketball history.

The team, led by seniors Christian Watford and Jordan Hulls, along with eventual top-five NBA draft picks Victor Oladipo and Cody Zeller, advanced to the Sweet Sixteen in the NCAA tournament before losing to eventual Final Four participant Syracuse.

Despite these low finishes and player arrests,[27] Crean was retained after appearing on many media "hot seat" lists.

[1] For inspiration, Crean has a library filled with biographies of coaches and business executives, with favorites being Jim Collins' management guide "Good to Great" and the story of Bill Belichick's rise in New England, "Patriot Reign".

[1] During his time at Indiana, Crean was criticized by fans and local sports media for the amount of turnovers his teams committed,[39] poor defense,[40] lack of team fundamentals, poor in-state recruiting,[41] large numbers of players transferring,[42] and his "blow-by" handshakes of opposing coaches.

In 2004, he served as an assistant coach for USA Basketball's under-20 team in the FIBA Americas World Championship.