In January 2004, he was signed by fellow Serie A club U.C. Sampdoria on loan with option to co-own the player, which the club did in June 2004, for €500,000. He scored his first Serie A goal against A.S. Roma, which gave the team a 1–0 lead, but the game ended in 1–1 draw after Francesco Totti scored a penalty 3 minutes later, in 2004–05 Serie A. He was loaned back to Atalanta in January 2005. Atalanta were relegated at the end of the season, so Pagano went on loan to Bari instead of staying with the "Nerazzurri".