Méndez started his career with Vélez Sársfield in 1993. During his time with Vélez the club had their most sustained period of success in their history. They won 3 league titles and 5 international tournaments.
In 2002 Méndez moved to Spain to play for Celta Vigo.
In 2006 Méndez returned to Argentina to play for San Lorenzo, in 2007 he helped San Lorenzo to win the Clausura 2007 tournament. His fourth league title.