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. This was the 52nd season in which an NCAA ice hockey championship was held and is the 105th year overall where an NCAA school fielded a team.

The 1999–2000 NCAA Division I men's ice hockey season began on October 1, 1999, and concluded with the 2000 NCAA Division I Men's Ice Hockey Tournament's championship game on April 8, 2000, at the Providence Civic Center in Providence, Rhode Island. This was the 53rd season in which an NCAA ice hockey championship was held and is the 106th year overall where an NCAA school fielded a team.