He started coaching on 1 October 1999, with Puebla FC. Later, he worked as an assistant coach for Pumas UNAM, under head coach Hugo Sánchez, becoming champions for two consecutive tournaments. Mario is known for his strong defensive, and fast offensive playing scheme, and always encouraging his players to never give up. He spends long hours studying rivals, hence gaining the nickname of "Capello", in reference to Italian head coach Fabio Capello's skills.
In 2005, Club América won the Mexican Clausura championship under Carrillo management,[1] that being to date his biggest accomplishment.
Later, Carrillo moved to La Liga of Spain to join Javier Aguirre as an assistant coach of Atlético Madrid.
After the FIFA World Cup of South Africa 2010, he returned to Mexico, to manage Pumas UNAM.
Mexico National Team
He was Assistant Coach of Manuel Lapuente in the Mexico national team during the FIFA World Cup of France, in 1998.
He was also invited by Javier Aguirre to be his Assistant Coach in the Mexico national team, for the FIFA World Cup South Africa 2010 project.