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 104th year overall where an NCAA school fielded a team.