He reached the peak of his career in the 1996–97 season when he joined Serie A team A.C. Milan after spells with Sampdoria and Pistoiese. Giorgio Morini originally planned to use Pagotto as his first choice goalkeeper, but by the end of the season he was only second-choice behind Sebastiano Rossi. He spent just one season at Milan, making eight league appearances in the process, before moving on to fellow Serie A side Perugia.
Following a short stay at the Stadio Renato Curi, Pagotto had spells at Empoli and Reggiana in Serie B before returning to Perugia for another season. After his second run at the Umbrian outfit, he dropped down two divisions to play for the Serie C1/A side Triestina and was instrumental in their successful 2001–02 season that saw them finish runners-up and earn promotion to the Serie B.
He spent another season at Triestina, helping them finish 5th in their first season in Serie B since the 1990–91 season before dropping back down a division with Arezzo. Arezzo conceded just 27 times in 34 games in the 2003–04 season (with Pagotto playing on 30 occasions in the league) as they marched to the title, something Pagotto just missed out on two seasons earlier with Triestina. He remained their first choice goalkeeper in Serie B as Amaranto survived relegation.
Pagotto was the first-choice goalkeeper for the Italy Under 21s national side between 1994 and 1996. He is a two-time winner of the UEFA European Under-21 Championship, both times under the guidance of then manager Cesare Maldini. He notched a total of ten caps for the Azzurrini. However, he was never capped with the Italian national team.
On 28 April 2007, just before a game in the Serie B between Pagotto’s Crotone and Spezia, Pagotto tested positive for cocaine. He pleaded guilty at a hearing on 30 July and was banned from professional football for life. He appealed and, on 14 September, his sentence was reduced to eight years. The ban expired on 2015, when he was 41.