Georgia Southern Athletic Director Tom Kleinlein announced the coaching change after the Eagles finished the season 14-19 overall and 7-11 in the Southern Conference.
"Charlton Young represents Georgia Southern with the utmost character. He has done a tremendous job with taking a program that had some trouble when he arrived and getting it to a level of respectability," Kleinlein said.
"At the same time, I felt where we needed to go is beyond where we are at right now and that a change in leadership is necessary."
Georgia Southern was a combined 48-84 overall and 26-46 in the conference in Young's four seasons as coach.
Young, 41, was a three-time all-conference pick while as player at Georgia Southern. He owned the school record in assists with 570 when he graduated.