The 1998–99 NCAA Division III men's ice hockey season began in October 1998 and concluded on March 20 of the following year. This was the 26th season of Division III college ice hockey.
Division II Findlay joined with 4 Division III schools to form the MCHA. After the season the Oilers jumped up to Division I but were allowed to immediately participate in postseason tournament because they officially remained a D-II program.
Championship: March 10, 1999 † indicates conference regular season champion * indicates conference tournament champion ‡ a game between Assumption and Worcester State was cancelled.
Championship: February 27, 1999 † indicates conference regular season champion * indicates conference tournament champions Lawrence played their entire Division III schedule against MCHA schools but did not formally join the conference until 1999-2000
Championship: March 6, 1999 † indicates conference regular season champion * indicates conference tournament champion Bemidji State was ineligible for Division III tournaments