The 1998–99 Mount St. Mary's Mountaineers men's basketball team represented Mount St. Mary's University during the 1998–99 NCAA Division I men's basketball season.

The Mountaineers, led by head coach Jim Phelan, played their home games at Knott Arena and were members of the Northeast Conference.

They were champions of the NEC tournament to earn an automatic bid to the NCAA tournament.

16 seed in the Midwest region, the Mountaineers lost to No.

1 seed and eventual Final Four participant Michigan State in the Round of 64.