Pitino had three years remaining on a six-year deal he signed with Louisville in March 2001.
"I'm so delighted that Rick has agreed to remain our men's basketball coach for an additional three years," Athletic Director Tom Jurich said. "When he became our coach, I felt that if he could reconstruct our program in six years, it would be a major coup."
Pitino's name had been floated for the vacant job at St. John's, which fired Mike Jarvis on Dec. 19. Pitino is 415-151 in 18 years of college coaching, including stops at Boston University, Providence and Kentucky. He captured the 1996 national title with the Wildcats.
He also had stints in the NBA coaching the New York Knicks and the Boston Celtics.