hired Johnson as head coach of Cardinal men's basketball on May 25, 2004. In his four seasons at Stanford, Trent Johnson had a record of 80–48. He led the Cardinal to three appearances in the NCAA tournament and one NIT appearance. Johnson's 2007–08 team advanced to the Sweet 16 as a No. 3 seed before finishing with a 28–8 overall record. He was named Pac-10 Coach of the Year following the regular season. Johnson's teams also reached NCAA Tournament in 2005 and 2007.
LSU
On April 10, 2008, Johnson left Stanford and was named the 20th head coach of LSU Tigers men's basketball. Johnson would go on to win the SEC Coach of the Year award during his first season after compiling a 13–3 regular season record and outright SEC regular season title. His 26–7 overall record, along with the SEC title, would be enough to earn his team its first NCAA tournament berth since 2006. The next two years resulted in poor finishes with 11–20 records both seasons. The 2011–12 season was better as LSU finished 18–14 and received an NIT bid.
TCU
Johnson resigned as head coach at LSU to be named head coach at Texas Christian University on April 9, 2012, heading into TCU's inaugural season in the Big 12 Conference after moving from the Mountain West Conference. In four seasons, Johnson went 50–79 at TCU, and his teams never finished higher than ninth in the Big 12. TCU went winless in Big 12 play in the 2013–14 season. However, Johnson's tenure at TCU included some upsets of top-25 teams, including a 62–55 home upset of #5 Kansas on February 6, 2013. In the 2014–15 season, TCU began the season 13–0 and made the 25th spot on the AP Poll for the week of December 22, for the program's first top-25 ranking in 16 years. TCU finished 18–15 that season after going 4–14 in Big 12 play. This would be Johnson's only winning season at TCU. On March 13, 2016, TCU fired Johnson.
Louisville
On October 11, 2017 the University of Louisville hired Johnson to fill the assistant coach opening created by new Louisville head coach David Padgett's promotion. Trent Johnson signed a nine-month contract to join David Padgett's interim staff. Louisville will pay Johnson $300,000 in salary in a deal that runs through June 30, the customary last day of men's basketball contracts at Louisville. Johnson was not retained as assistant coach by new head coach Chris Mack following the season.