[1] At 18 years of age, Muñoz made his league debut with Boca Juniors during a 0–1 defeat to Estudiantes de La Plata during the 2009 Clausura tournament.
[5] He made his debut with the Sicilian club on 26 August 2010, when he was picked as a starter in the return leg of the 2010–11 UEFA Europa League play-off round against NK Maribor.
[9] On 8 August 2017, Muñoz switched teams and countries again, signing a three-year deal with La Liga side CD Leganés, for a rumoured fee of € 2 million.
[10] Ten days later he made his debut for the club, starting in a 1–0 home win against Deportivo Alavés.
In 2009, Muñoz was called by the Argentina national team coach Diego Maradona for a friendly match against Panama in a squad exclusively formed with footballers based on the Argentine league.