Pérez debuted in the Mexican Soccer League with Necaxa in the 1999 Invierno season, playing his first game 21 September in a 3–1 victory against Santos Laguna. Pérez finished the season having played in 11 games, and by the beginning of the next year had a firm grip of the starting position. Pérez was named rookie of the tournament at the end of the season. Pérez played the next four years with Necaxa, until, to the surprise of many, was sold to Monterrey for the Clausura 2003, where he led Monterrey to win the championship by defeating Morelia at Estadio Morelos in Morelia. In the championship season, Pérez appeared in 23 matches, scored two goals and registered an assist. As with Necaxa, Pérez has been in the Monterrey lineup since his arrival.