Girls
Basketball: Lee Academy's girls' basketball program features a varsity and junior varsity Team. Girls' varsity competes in the Northern Maine Class C division and are a member of the Penobscot Valley Conference. Their regular season schedule consists of 18 games. Girls' junior varsity's regular season schedule ranges from 10-14 games.
Boys
Basketball: Lee Academy's boys' basketball program features a varsity and junior varsity team. Boys' varsity competes in the Northern Maine Class C division and are a member of the Penobscot Valley Conference. Their regular season schedule consists of 18 games. Boys' junior varsity's regular season schedule ranges from 14-16 games.
Co-Ed
Cheering: Lee Academy's cheerleading squad may compete in the Penobscot Valley Championship, Northern Maine Class D Championship, and State of Maine Class D Championship depending on ranking during the season. Cheerleading is open to both boys and girls. Alongside their competition season Lee Academy's cheerleaders also cheer at home varsity basketball games.
Wrestling: Lee Academy co-ops with Mattanawcook Academy to form a wrestling team.
Indoor Track: Lee Academy allows individuals to practice and travel with Mattanawcook Academy to compete as Lee Academy athletes. Their regular season consists 6-8 meets.