The Francis Marion Athletic Department offers 12 intercollegiate sports: baseball, basketball, cross country, golf, soccer, and tennis for men; and basketball, cross country, soccer, softball, tennis, and volleyball for women. The Patriot golf and women's soccer programs compete as NCAA Division I independents, while the remaining 10 sports compete in the NCAA Division II Peach Belt Conference.
The Patriot athletic program has twice earned the Commissioner's Cup award, signifying the best all-around athletic program in the Peach Belt Conference. The school regularly ranks among the conference leaders in student-athletes named to the PBC Presidential Honor Roll.
Despite its relative youth (founded in 1970), the Patriot athletic program has a rich and storied tradition, including five national championships and 48 conference or district titles. The golf program captured the 2003 NCAA Division II national title, while the women's tennis duo of Lee Whitwell and Mary Hirst won the 1993 and 1994 NCAA Division II doubles national championships. The women's basketball program captured the 1982 AIAW Division II national title and the 1986 NAIA championship. In addition, the 1987 Patriot softball team advanced to the NAIA national title game, but fell 1-0. Francis Marion has been represented by student-athletes in NCAA Division II national tournament competition every year since moving to NCAA membership in 1992.
Francis Marion graduate and former hoop player Pearl Moore holds the all-time women's college basketball scoring record with 4,061 points. The ball she used to break the previous career mark is displayed in the Naismith Memorial Basketball Hall of Fame in Springfield, Mass. Current University of North Carolina women's basketball coach Sylvia Hatchell headed the FMU program for 11 seasons (1975-86) prior to moving to Chapel Hill.
The FMU Athletic Hall of Fame includes 31 members, representing 11 different sports.
Francis Marion has an active chapter of Chi Alpha Sigma, the National College Athlete Honor Society.