In total, Pessotto was capped 22 times for Italy between 1996 and 2002, under managers Arrigo Sacchi (1996), Cesare Maldini (1996–98), Dino Zoff (1998–2000), and Giovanni Trapattoni (2000–2002). He played for his country at the 1998 FIFA World Cup, where Italy were eliminated by hosts and eventual champions France on penalties in the quarter finals, and at Euro 2000. At Euro 2000, Pessotto scored a penalty in the semi-final shootout win over co-hosts the Netherlands, which sent Italy into the final against France. In the final, Pessotto would set up Delvecchio's goal; however, he only picked up a runners-up medal, as Italy lost to France for the second consecutive tournament, after conceding a last minute equaliser, and then subsequently conceding a David Trezeguet golden goal. Trezeguet became his Juventus teammate the following season. He was unable to take part at the 2002 World Cup with Italy due to injury.