Stocco began his career in 2003 as a backup to Jim Sorgi, with limited action in only three games with 17 attempts and 10 completions. Stocco was promoted to the starting position at the beginning of the 2004 NCAA Division I-A football season. Stocco was a steady leader, guiding the Badgers to a 9-0 start and as high as #4 in the national rankings. Stocco was limited as a passer, with the Badgers rushing game providing most of the offense behind running back Anthony Davis and a strong defense led by All-American defensive end Erasmus James. 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. The Badgers accepted a bid to the Outback Bowl, where they were defeated by Georgia, 24-21. Stocco completed 52.6% of his passes.