Pérez began his professional playing career with Godoy Cruz, where he wrote his name into club history by scoring a fifth minute goal in the 1–1 draw with Belgrano on 9 September 2006. This was the first goal ever scored by Godoy Cruz in the Argentine first division. In total he has scores 9 goals in his career, most of them on penalty shots. In 2007, Pérez joined Estudiantes de La Plata, where he finished as runner-up with the team in the 2008 Copa Sudamericana. He was then a first team regular in the team that won the 2009 Copa Libertadores.
In June 8, 2011, he has agreed a five-year contract with Benfica for a fee rumored to be around 5.5 Million euros for 100% of his rights to Estudiantes de La Plata.