The 1998–99 Creighton Bluejays men's basketball team represented Creighton University during the 1998–99 NCAA Division I men's basketball season. The Bluejays, led by head coach Dana Altman, played their home games at the Omaha Civic Auditorium. The Jays finished with a 22-9 record, and won the Missouri Valley Conference tournament to earn an automatic bid to the 1999 NCAA tournament.