The Hatters compete in the NCAA Division I Football Championship Subdivision (FCS) and are primary members of the Atlantic Sun Conference for most sports, excluding the university's football program, which competes in the Pioneer Football League.

A member of the ASUN Conference (ASUN) since 1985, Stetson University sponsors teams in eight men's and ten women's NCAA sanctioned sports.

In 1948, Grace Lenczyk won the women's individual intercollegiate golf championship (an event conducted by the Division of Girls' and Women's Sports (DGWS) — which later evolved into the current NCAA women's golf championship).

Stetson had Varsity wrestling for 3 years (1983-1986).

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