| Division: | II |
| Year: | 1999 |
| Gender: | Men's |
| Teams: | 48 |
| Finalfourcity: | Commonwealth Convention Center Louisville, Kentucky |
| Champions: | Kentucky Wesleyan |
| Titlecount: | 7th |
| Runnerup: | Metro State |
| Gamecount: | 1st |
| Semifinal1: | Florida Southern |
| Finalfourcount: | 6th |
| Semifinal2: | Truman |
| Finalfourcount2: | 1st |
| Coach: | Ray Harper |
| Coachcount: | 1st |
| Mop: | Antonio Garcia |
| Mopteam: | Kentucky Wesleyan |
The 1999 NCAA Division II men's basketball tournament was the 43rd annual single-elimination tournament to determine the national champion of men's NCAA Division II college basketball in the United States.
Officially culminating the 1998–99 NCAA Division II men's basketball season, the tournament featured forty-eight teams from around the country.
The Elite Eight, national semifinals, and championship were again played at the Commonwealth Convention Center in Louisville, Kentucky.
Kentucky Wesleyan (35–2) defeated Metro State in the final, 75–60, to win their record seventh Division II national championship. This title came one year after the Panthers' loss to UC Davis in the 1998 championship.
Kentucky Wesleyan was coached by Ray Harper. For the second consecutive year, KWC's Antonio Garcia was the Most Outstanding Player.
Location: Recreation and Convocation Center Host: College of Saint Rose
Location: Gerald Stockton Court Host: Midwestern State University
Location: T. Edward Davis Gymnasium Host: Salem-Teikyo University
Location: Rice Auditorium Host: Wayne State College
Location: Centennial Center Host: Georgia College & State University
Location: Sportscenter Host: Kentucky Wesleyan College
Location: Bruce Hall Host: LeMoyne-Owen College
Location: Nicholson Pavilion Host: Central Washington University
Location: Commonwealth Convention Center Host: Bellarmine College