The university made the announcement Tuesday morning.
Though Martelli, 64, is the winningest coach in Hawks history, he just concluded his third straight season without a winning record.
Martelli has three NCAA Tournament appearances in the last 11 years (2008, 2011, 2014).
He has led the Hawks to seven total NCAA Tournaments since taking the helm in 1995. In 2003-2004, the team was undefeated in the regular season, 27-0, and went to the Elite Eight. Martelli was named Naismith College Coach of the Year.
The university said it will begin a search for a new head coach immediately.
The statement from Saint Joseph's University reads:
"Today, Saint Joseph's University announced its decision to make a leadership change in its men's basketball program. The University will immediately begin a search for a new head coach, with the goal of filling the position in the coming weeks.
Coach Phil Martelli stands out among his peers in college basketball not only for his long tenure and the many accolades that he and his teams have achieved, but also for his engagement with the community and his service as an ambassador for SJU. The University recognizes and celebrates the history and heart that Coach Martelli brought to the program and thanks him for his long service, dedication and stewardship.
As basketball is an important strategic asset for Saint Joseph's, the University will move forward with the intent to build upon its storied history, develop a sustained culture of excellence, and consistently compete for NCAA tournament appearances and conference championships."
This article has been corrected to show the Hawks have made three NCAA Tournament appearances since 2008.