A journeyman with eleven different clubs in his career, Pecchia amassed over 300 first division appearances. He began his career with Avellino in 1991, and remained at the club for two seasons. Despite heavy interest from Parma, he moved to Napoli in 1993, where he played for four seasons, becoming a key figure for the club, although he later struggled to establish himself in other teams. He made his Serie A debut with the Neapolitan club on 29 August 1993, at the age of 20, becoming a vital member of Marcello Lippi's midfield; Pecchia's tactical versatility, speed, technique, vision, and passing range allowed him to excel in Lippi's offensive tactical system, which made frequent use of long balls and fast-paced football. With Napoli, Pecchia soon established himself as one of the most promising and talented young Italian stars of the 90s, due to his leadership and work-rate; during his first season with Napoli, he helped the club qualify for the UEFA Cup. He remained at the club for three more seasons, despite the club's financial difficulties and lack of success during this time. During the 1996–97 season, he was named Napoli's captain, and he helped the club to reach the 1997 Coppa Italia Final under manager Luigi Simoni, in which Napoli was defeated by Vicenza in extra time; during the first leg of the final, Pecchia scored Napoli's winning goal. Despite his attachment to the club, he was sold to Juventus in 1997 for 10 billion Lit., in an attempt to manage the club's debts; he would later return to Napoli, on loan, however, for a single season, in 2001. In total, he made 152 appearances for Napoli, scoring 21 goals.