Perez made his debut with the Mexico national team 17 November 1998 in a friendly against El Salvador in Los Angeles. Uncapped through the next two years, he reemerged in 2000. His first official tournament was the 2001 FIFA Confederations Cup, where Mexico did not win any matches. Pérez made appearances for the team in the Gold Cup in 2003, and playing for the U-23 team in the 2004 Summer Olympics. Pérez appeared in the 2005 FIFA Confederations Cup where he played in all five matches, including assisting Jared Borgetti in a losing effort against Germany in the third place match. Pérez was included by then coach Ricardo Lavolpe in the 2006 FIFA World Cup squad. He came on in the 45th minute for Gerardo Torrado in the first match against Iran. Pérez did not appear in the second match against Angola, which Mexico and Angola drew 0–0, however he started the third match against Portugal, but he was sent-off in the 61st minute. Mexico lost the match 2–1. He was banned for the round of 16 match against Argentina because of his red card against Portugal.