In 2006, Muñoz was promoted to first–team of Santiago Wanderers, a club he had been a part of since he was five years of age. He made two appearances in his first season with the first team. The next year he found more space, become the clubs second choice striker for the most part and bagged two goals in 14 appearances. His third year was a further improvement, playing in even more games (18) and scoring three goals. The 2009 year was a poor one for the striker where he struggled with injuries and form. The 2010 season was Carlos Muñoz real breakout season. He was the first choice striker all season and in 34 first team appearances he scored on 17 occasions. His form continued into 2011 and in the first half of the year he scored eight times in 16 appearances.
His goals led him to be called up to the Chilean national team for the first time early in 2011.
His form over the last year and a half earned him a move to Colo-Colo in June 2011 who spent US$1.5 million to bring him in.
After scoring 35 times in 74 appearances over two season at Colo-Colo, Muñoz signed for Emirati football club Bani Yas SC.