The 2012–13 Jacksonville Dolphins men's basketball team represented Jacksonville University during the 2012–13 NCAA Division I men's basketball season.

The Dolphins were members of the Atlantic Sun Conference (A-Sun).

They were led by head coach Cliff Warren, and played their home games in both the Veterans Memorial Arena and Swisher Gymnasium.

They finished the season 14–18, 9–9 in A-Sun play to finish in a three way tie for fourth place.

They lost in the quarterfinals of the Atlantic Sun tournament to USC Upstate.