After playing for the Veloce Calcio di Savona youth side, Panucci started his professional career with Genoa in 1990, and made his Serie A debut with the club during the 1991–92 Serie A season; following his impressive performances during the 1992–93 season, which saw him score 3 goals in 30 appearances, he moved to A.C. Milan in July 1993, at the age of 20. A talented prospect, he was originally brought in as a younger, more attack-minded alternative to the incumbent right-back Mauro Tassotti, who had held the position for over a decade, and was expected to be a back-up. However, Panucci began to work his way into the starting lineup under manager Fabio Capello, appearing in 19 league matches and scoring twice as Milan won domestic and European titles. He also demonstrated his versatility by lining up at left-back in the 1994 UEFA Champions League Final, while Tassotti played on the right, and Paolo Maldini and Filippo Galli in the centre, filling in for the injured Franco Baresi and the suspended Alessandro Costacurta, who were normally the club's starting central defensive pair; despite several important absences, Milan defeated Barcelona 4–0 to win the title. Nonetheless, it was Tassotti, not Panucci, who traveled to the United States that summer as part of the Italian World Cup selection under Arrigo Sacchi. For his performances, Panucci won the Bravo Award, as the best Under-23 player in Europe.