Perrotta was eligible to play for both Italy and England – the latter due to his birth in the country (in addition to being Italian, he is automatically a British citizen as the United Kingdom granted unconditional birthright citizenship until 1983). Perrotta made his debut for the Italy under-21 team under Marco Tardelli, making 6 appearances and scoring a goal. He won the 2000 UEFA European Under-21 Football Championship, appearing in Italy's 2–1 victory over the Czech Republic in the final, but was later dropped from the 2000 Summer Olympics squad due to injury. He made his senior international debut under Giovanni Trapattoni, on 20 November 2002, in a 1–1 draw against Turkey. He subsequently played for Italy at UEFA Euro 2004, scoring a goal in a 2–1 win against Bulgaria, although the Italian national side were eliminated in the first round of the tournament on direct-encounters following a three-way five point tie with Denmark and Sweden.