Stocco was the most experienced quarterback in the Big Ten entering his senior year in 2006, which was the rookie season for Bret Bielema. Stocco struggled with a new core of receivers, culminating in a loss to Michigan in Week 5. The Badgers got back on track and in sync as the season progressed, behind the legs of freshman sensation P. J. Hill, Jr., as the Badgers won their final eight games. During this time, Stocco's consecutive starts streak ended when he was injured in a home game against Penn state; however, the Badgers reached the top ten in the rankings and again accepted a bid to the Capital One Bowl, where they defeated Darren McFadden and the Arkansas Razorbacks. Stocco threw for 206 yards and two crucial touchdowns in the gritty 17-14 win, and was named the game's Most Valuable Player in his final collegiate game. The Badgers ended the season 12-1 and with a #7 ranking.