The 1988–89 NCAA Division III men's ice hockey season began in October 1988 and concluded on March 25 of the following year. This was the 16th season of Division III college ice hockey.
Championship: March 11, 1989 † indicates division regular season champions ~ indicates division tournament champions * indicates conference tournament champion
Championship: March 4, 1989 † indicates conference regular season champion * indicates conference tournament champions ^ Plattsburgh State voluntarily ruled themselves ineligible for postseason play while they were under investigation for NCAA rules violations