The following season (2003–04), Pellissier made 27 league appearances and scored three goals, two of which were scored against Siena in a 2–1 victory, and marked his first brace. During the 2004–05 season, he scored seven times in 34 appearances. He scored twice in a 3–1 victory against Brescia. 2005–06 was Pellissier's breakout season; he made a significant contribution to Chievo's campaign, scoring 13 of Chievo's 54 league goals. Among them, Pellissier scored in four consecutive matches and twice in the matches against U.S. Lecce and Reggina Calcio. The season was an important one; the 2006 Italian football scandal ensured that Chievo finished in fourth place because of various points deductions to other sides, qualifying Chievo for the 2006–07 UEFA Champions League.