Muñoz's first international cap for Mexico was in a friendly match against Ecuador on 27 October 2004. Muñoz was the second-choice goalkeeper at both the 2004 Copa América and the 2005 Confederations Cup. Muñoz was the starting goalkeeper during the 2005 CONCACAF Gold Cup. Coach Ricardo La Volpe included him in the preliminary squad for the 2006 World Cup, but he did not make the final 23-man list. Muñoz had also been called up as a backup goalkeeper by Hugo Sánchez and Sven-Göran Eriksson.