All middle School students and fourth-and-fifth grade boarders must participate four days per week in the school's organized team sports or physical education programs (P.E). Aiken Prep fields varsity teams in soccer, volleyball, basketball, baseball, tennis, and golf. The physical education program exposes students to a variety of traditional and nontraditional activities- including cooperative games, air rifle shooting, ultimate frisbee, fencing, rock climbing, touch rugby, and the occasional pickup cricket game. Athletic facilities include a gymnasium, an outdoor swimming pool, tennis courts, and three playing fields. Students enjoy golfing privileges at the nearby Palmetto Golf Club.

"Colors" are awarded at the end of each season to team members who demonstrate good effort, participation, and sportsmanship. Sports Day is held annually, with track and field events and awards for each division. Junior and Senior Athletes of the Year are recognized each spring, along with the most outstanding athlete on each team.