The Paladins posted a 7-24 record and 3-15 Southern Conference mark this past season under Jackson, who compiled an 85-131 overall record in seven seasons at the helm of the Furman program.
Furman won 22 games just two seasons ago and advanced to the CollegeInsider.com Tournament.
"I would like to take this time to thank everyone in the Furman community for the support they showed our program, especially Dr Clark and President Smolla," said Jackson in a written statement. "I am very grateful for the opportunity I was given to coach at Furman."
Two of the higher profile wins for the Paladins during Jackson's tenure came in 2006 against Vanderbilt and South Carolina in 2010.
Furman athletics director Dr. Gary Clark says a search for a new basketball coach will begin immediately.