Mooney began his coaching career fresh out of college at
Lansdale Catholic High School in
Lansdale, Pennsylvania. In 1998, Mooney took the helm of the program at Beaver College, now known as
Arcadia University. After two years at Beaver, Mooney took an assistant coaching position under
Joe Scott at the
United States Air Force Academy. When Scott left to take the head coaching position at
Princeton University in 2004, Mooney was elevated to the head position at Air Force. After one season at Air Force, Mooney became head coach at the
University of Richmond. The University of Richmond announced on March 27, 2011, following a run to the Sweet Sixteen in the
2011 NCAA Division I men's basketball tournament that Mooney had signed a new contract running through the 2020–21 season. With an 84–74 win over
Wake Forest on December 1, 2018; Mooney tallied his 240th win at Richmond, vaulting him past
Dick Tarrant to become the winningest coach in Richmond history. On February 17, 2023, Richmond announced that Mooney would miss the remainder of the 2022–23 season due to heart surgery to address an aneurysm in his ascending aorta. Assistant coach and former Richmond player Peter Thomas served as interim head coach in Mooney's absence. Mooney returned to the bench shortly after the conclusion of the season. ==Head coaching record==