The university sponsors 20 varsity sports teams including men and women's basketball, cross country, golf, soccer and tennis; women's-only dance team, equestrian, beach volleyball, softball, track and field and volleyball; men's-only baseball; and co-ed sailing and cheerleading.

[4] The men's basketball team won the NAIA national title in 1983 and made four trips to the NCAA Tournament (1994, 1997, 1998 and 1999) under the leadership of former head coach John Kresse.

In 2006, the college welcomed Bobby Cremins, who led Georgia Tech to the Final Four, as its new head basketball coach.

The Cougars returned to the NCAA Tournament in 2018 under Earl Grant, and in back-to-back years under Pat Kelsey, 2023 and 2024.

They have made the Women's Basketball Invitational in 2010, 2013, and 2014 The College of Charleston baseball team was the 2004, 2005, 2007 and 2012 SoCon regular season champion.

In 2006, the Cougars won the regular season championship and the postseason tournament before advancing to their first-ever NCAA Super Regional.

The Cougars have been to seven NCAA Regionals- all since 2004- and have had 61 players sign professional contracts, including New York Yankees starting left fielder Brett Gardner.

The Cougars have been successful in the beach volleyball arena, qualifying for the first AVCA National Championship in 2012, finishing fourth.

In the 2016 season, with the NCAA sponsoring an official national championship for the first time, the Cougars competed as an independent.