The 1998–99 NCAA Division I men's ice hockey season began on October 3, 1998, and concluded with the 1999 NCAA Division I Men's Ice Hockey Tournament's championship game on April 3, 1999, at the Arrowhead Pond of Anaheim in Anaheim, California.

The 1998-99 season was the inaugural year for Metro Atlantic Athletic Conference's hockey division.

All five teams had been part of ECAC lower classifications in the past (as had Canisius, Fairfield and Iona) and were promoted to Division I for the 1998-99 season.

Note: * denotes overtime period(s) [3] The following players led the league in points at the conclusion of the season.

GP = Games played; G = Goals; A = Assists; Pts = Points; PIM = Penalty minutes [4] The following goaltenders led the league in goals against average at the end of the regular season while playing at least 33% of their team's total minutes.