| Mode: | Basketball |
| Year: | 1998–99 |
| Team: | Charleston Cougars |
| Conference: | Southern Conference |
| Division: | South Division |
| Short Conf: | SoCon |
| Aprank: | 16 |
| Record: | 28–3 |
| Conf Record: | 16–0 |
| Hc Year: | 20th |
| Champion: | SoCon Regular season champion SoCon tournament champion |
| Tourney Result: | first round |
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. 8 seed in the East region. 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. 16 in the final AP poll.
|-!colspan=12 style=| Regular season
|-!colspan=12 style=| SoCon tournament|-!colspan=12 style=| NCAA TournamentSource[2]
See main article: 1998–99 NCAA Division I men's basketball rankings. [3]