He served a two-year stint, 1987–1988, as offensive line coach at Northern Arizona University and one year as offensive coordinator of Southern Illinois in 1989. From 1990–1994, Callahan was offensive line coach at the University of Wisconsin–Madison. He has been praised by former Wisconsin coach Barry Alvarez as being one of the primary reasons why the Badgers were able to turn their program around and eventually win three Rose Bowls in the 1990s. Alvarez cited Callahan specifically for his strong recruiting abilities.