In 2004-2005, he worked as an administrative assistant under Tom Herrion at the College of Charleston. In 2005, he was hired by coach Ron Everhart to serve as assistant coach at Northeastern University and followed Everhart to Duquesne University the following year. He was hired on at Louisville in October. In his first stint with the Cardinals, he helped them advance to back-to-back NCAA Elite Eight appearances. He left the University of Louisville and accepted a position to work under Billy Donovan at the University of Florida on April 17, 2009. During his time at Florida, they advanced to two NCAA tournaments including one Elite Eight appearance in 2010. He left Florida on April 12, 2011, to become the associate head coach at Louisville. In his second stint at the school he helped the Cardinals advance to the NCAA Final Four and finish with a 30-10 overall record.
Pitino left his position as the associate head coach at Louisville to become the head coach at FIU on April 15, 2012 replacing Isiah Thomas. With only six players remaining from the previous season, and not all of them on scholarship, Pitino cobbled together a team and coached a high-pressure defense that finished eighth in the nation in steals. He was able to compile an 18-14 record in his first season as head coach. This was FIU's first winning season since 1999-2000 and most wins overall since 1997-98. His FIU team also had the best conference record in school history. Additionally, FIU reached the Sun Belt Tournament Title game as a four seed, before falling to Western Kentucky in the tournament championship game, 65-63.
Minnesota
On April 3, 2013, despite having only one year of head coaching experience at FIU, Pitino was hired to become the 17th head coach in University of Minnesota history, replacing Tubby Smith. On April 1, 2014, in Pitino's first season at Minnesota, the Golden Gophers defeated Florida State University 67–64 in overtime in the NIT semifinals, breaking a school record with its 24th win of the season. On April 3, 2014, exactly one year to the date he was hired, Pitino won his first NIT Championship by defeating coach Larry Brown's SMU team 65–63, securing a school record 25th win. The win was the Gophers first NIT championship since 1998 - although that was vacated in 1999 - and their first "official" NIT title since 1993. Following a historically bad third-year at Minnesota, Coach Pitino orchestrated an impressive turnaround by improving the team's record by 16 wins, utilizing a revamped roster that included five new contributors. The turnaround helped earn Richard Pitino the Big Ten Coach of the Year award on March 6, 2017. This was just the second Big Ten coach of the year award in Minnesota school history, and Minnesota's first since 1982. That season Pitino guided the Gophers to an 11-7 record in the Big Ten, which was Minnesota's most wins in conference in 20 years. On March 21, 2019, in the first round of the 2019 NCAA Men's Division I Basketball Tournament, No. 10 Minnesota faced No. 7 seed Louisville, a school he previously helped coach and a program which his father Rick had been head coach of for 16 years. Minnesota defeated the Cardinals 86–76 to move on to the Round of 32. In the Round of 32, the Gophers lost to #2 Michigan State 70-50.