The 1998–99 Nebraska Cornhuskers men's basketball team represented the University of Nebraska, Lincoln during the 1998–99 college basketball season.

Led by head coach Danny Nee (13th season), the Cornhuskers competed in the Big Twelve Conference and played their home games at the Bob Devaney Sports Center.

They finished with a record of 20–13 overall and a 10–6 record in Big Twelve Conference play.

Senior center Venson Hamilton was named the Big 12 Player of the Year.

Nebraska played in the National Invitation Tournament, and advanced to the second round.