Fortunato started his professional career as a left-back with the Como first team in 1988, at the age of 17, making his Serie B debut with the club on 29 October 1989, in a 1–0 home win against Cosenza. The young player from Salerno played 16 times with the Lariani in his first season, who were relegated to Serie C1. He soon established himself into the team's starting line-up the following season, making 27 appearances in the league, as Como narrowly missed out on promotion to Serie B, losing out in the playoff to Venezia. Fortunato's consistent performances caught the eye of bigger Italian clubs – most notably Genoa. It was the Ligurian side who signed Fortunato in 1991; however, his limited opportunities with the club, due to the presence of the more experienced Branco in his role, led to an argument with Osvaldo Bagnoli's assistant manager Sergio Maddè. As a result, Fortunato was labelled as an "arrogant hothead", and was immediately loaned out to Serie B side Pisa for the 1991–92 season, where he made 25 appearances.