Stocco played football for the University of Wisconsin–Madison, starting at quarterback for the Badgers during his sophomore, junior and senior seasons.
Out of high school, he was drafted in the 45th round by the Major League Baseball team the Minnesota Twins, but decided to go to college instead.
With hopes of a Rose Bowl invitation, the Badgers collapsed down the stretch, ending the season with two losses to fall out of BCS contention.
In 2005, Barry Alvarez's final season, the Badgers' offense was considerably more potent, with All-American candidates Brian Calhoun, Brandon Williams, and Joe Thomas leading the way.
The Badgers reached as high as #12 in the rankings after an 8–1 start, but consecutive losses to Penn State and Iowa ended their Big Ten title hopes.
Stocco was the most experienced quarterback in the Big Ten entering his senior year in 2006, which was the rookie season for Bret Bielema.
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.