The 1999–2000 NCAA Division III men's ice hockey season began on October 22, 1999 and concluded on March 18 of the following year.
The NCAA began offering automatic bids for conference tournament champions for the first time.
Each team in the ECAC East and NESCAC played one another in one game that counted in their respective conference standings.
Because the NESCAC now sponsored ice hockey as a varsity sport, the conference dropped the policy that allowed member schools to play in only one postseason tournament.
Minnesota–Crookston joined the MCHA, despite being a Division II program, and met conference guidelines by not offering scholarships to any players.