In the 2006 NCAA Division II football season (organized by the National Collegiate Athletic Association), Fort Hays State Tigers changed from being part of RMAC to being with MIAA, and Kentucky Wesleyan Panthers changed from being part of Mid-South (NAIA) to GLFC.
The 2006 NCAA Division II football season, part of college football in the United States organized by the National Collegiate Athletic Association at the Division II level, began on September 2, 2006, and concluded with the NCAA Division II Football Championship on December 16, 2006 at Braly Municipal Stadium in Florence, Alabama, hosted by the University of North Alabama. Fort Hays State Tigers RMAC MIAA Kentucky Wesleyan Panthers Mid-South (NAIA) GLFC 
