The 1998–99 College of Charleston Cougars men's basketball team represented the College of Charleston during the 1998–99 NCAA Division I men's basketball season.

The Cougars, led by 20th-year head coach John Kresse, played their home games at F. Mitchell Johnson Arena in Charleston, South Carolina as first-year members of the Southern Conference.

After finishing atop the conference regular season standings with a peerless 16–0 mark, the Cougars also won the 1999 SoCon tournament – capping a 25-game win streak – to earn an automatic bid to the NCAA tournament as No.

College of Charleston was beaten in the opening round by Tulsa, 62–53.

[1] The team finished with an overall record of 28–3 and were ranked No.