Born in Buenos Aires, Rodríguez made his league debut for Boca Juniors in a 2–1 away defeat to Chacarita Juniors on December 10, 2000. He went on to establish himself as an important player in the Boca Juniors team that won a host of national and international tournament in the early 2000s. In 2003 he was part of the Boca team that won the Intercontinental Cup.
In 2004 he signed for Spartak Moscow, but returned to Boca on loan for the 2007 Clausura (spring championship). For the 2007–08 season he joined Spanish side Espanyol on loan.
On June 24, 2013, São Paulo signed Rodríguez to a two-year contract.
On April 7, 2014, after almost one year playing for São Paulo, Rodríguez, along with Fabrício, was removed from the main staff of the club, and sent on loan to Boca Juniors. Rodríguez, who had a contract with the club until June 2015, will therefore no longer play for São Paulo.