| Type: | NAIA |
| Year: | 2006 |
| Gender: | Men's |
| Division: | II |
| Teams: | 32 |
| Fabfourarena: | Keeter Gymnasium |
| Fabfourcity: | Point Lookout, Missouri |
| Champions: | College of the Ozarks Bobcats |
| Titlecount: | 1st |
| Champgamecount: | 2nd |
| Champffcount: | 2nd |
| Runnerup: | Huntington Foresters |
| Gamecount: | 1st |
| Runnerffcount: | 2nd |
| Semifinal1: | Lindenwood Lions |
| Fabfourcount1: | 1st |
| Semifinal2: | MidAmerica Nazarene Pioneers |
| Fabfourcount2: | 1st |
| Mvp: | Michael Bonaparte |
| Mvpteam: | College of the Ozarks |
| Hustle: | Doug Sheckler |
| Hustleschool: | Huntington (IN) |
| Topscorer: | Alex Kock |
| Topscorerteam: | Huntington (IN) |
| Points: | 121 |
The 2006 NAIA Division II Men’s Basketball national championship was held in March at Keeter Gymnasium in Point Lookout, Missouri. The 15th annual NAIA basketball tournament featured 32 teams playing in a single-elimination format.