Coach Kelly was named Cincinnati's head coach on December 3, 2006, following the departure of Mark Dantonio. Both Cincinnati and Central Michigan were preparing for bowl appearances so while Kelly was in Cincinnati preparing the Bearcats, much of his staff remained at Central Michigan to coach the Chippewas. Following Central Michigan's win in the Motor City Bowl most of his staff joined him in Cincinnati where they went on to coach Cincinnati to a victory over Western Michigan University in that year's International Bowl, 27-24. Entering the 2007 college football season, Coach Kelly is 1-0 in a partial season at Cincinnati.
Coach Kelly had to suspend an unnamed player during the off-season in the Spring of 2007 because of lying, a violation of school ethics.