Cincinnati
Kelly was named Cincinnati's head coach on December 3, 2006, following the departure of Mark Dantonio. In an unusual move, Cincinnati elected not to appoint an interim coach and asked Kelly to assume his duties immediately by coaching the Bearcats in their bowl game. Central Michigan was also preparing for a bowl appearance, 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 31–14 win in the Motor City Bowl on December 26, most of his staff joined him in Cincinnati, where they went on to coach Cincinnati to a 27–24 victory over Western Michigan University in that year's International Bowl on January 6. Cincinnati's victory gave Kelly the unique distinction of having defeated the same team twice in a season as coach of two different teams (Central Michigan had defeated Western Michigan 31–7 earlier that season).
In his first full season, Kelly led Cincinnati to a competitive position in the Big East; the Bearcats' second ever 10-win season (its first since 1949); and a Top 25 ranking. On December 5, 2007, Kelly was named Big East Coach of the Year after leading the Bearcats to a 9–3 record. Coach Kelly later led the Bearcats to a 31–21 victory in the PapaJohns.com Bowl over Southern Miss.
In 2008, Kelly led Cincinnati to its first ever outright Big East title with key wins over West Virginia and Pittsburgh. The Bearcats had never defeated either team in Big East conference play. Kelly also became the first coach to win all three of the Bearcats' traveling trophies— the Victory Bell (Miami ), the Keg of Nails (Louisville), and the River City Rivalry Trophy (Pitt). The Bearcats played in the Orange Bowl versus the ACC champion, Virginia Tech on January 1, 2009 but lost 20–7.
After beginning the 2009 season unranked in all polls, Kelly's Bearcats reeled off 12 straight victories and finished the regular season undefeated. Going into the bowl season, they were ranked #3 in the BCS Standings and faced the Florida Gators in the Sugar Bowl. Kelly did not coach the team in the loss to the Florida Gators because of his departure to Notre Dame.
Among the honors that Cincinnati football achieved in 2009 was the highest academic rating among teams in the top 10 of the current BCS standings, according to the 2009 Graduation Success Rates, released Wednesday, November 18, by the NCAA. Cincinnati, which was fifth in the BCS standings, checked in with a 75 percent NCAA graduation rate and a 71 percent federal government rate, the only team in the BCS top 10 to surpass the 70 percent plateau in both.
Kelly finished his tenure at Cincinnati with a 34–6 record.
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