Mario Méndez started his career with Club Atlas in the year 1998, in the golden age that included many (at the time, promising) players like Rafael Márquez, Daniel Osorno, Juan Pablo Rodriguez and Miguel Zepeda.

In 2004 Mario Mendéz was bought by Deportivo Toluca F.C., where he was an important player in the squad playing 49 games and scoring one goal.

Although he had been criticized for his occasional careless plays and teamwork abilities on the national team, he continuesd to be one of Mexico's important talented players.

During the Winter Transfer period, Ricardo Lavolpe, head coach of the Argentine Vélez Sársfield, called on the talents of Mario Méndez for Vélez Sársfield After Lavolpe's resignation as coach Mendez returned to Mexico, joining Club Toluca.

He appeared in the September 2008 friendly match against Chile (a 1–0 defeat), coming on as a substitute for Jaime Correa Córdoba.