Pérez spent the 2002 season as backup to Einar Diaz and was granted free agency at the end of the year. In January 2003, he signed a contract to play for the Milwaukee Brewers. Pérez was in a platoon system alongside Keith Osik in which he started three out of every five games. He was hitting for a .315 batting average by mid-season, but tapered off to finish the season with a .271 average along with career-highs in home runs (11) and runs batted in (45).