[4] Gerardo Flores began his football career with cross town club Zacatepec FC in Morelos, Mexico.
During his stay at Zacatepec, he would be called to the Mexican squad that would participate in the 2003 FIFA U-17 World Championship held in Finland by coach Julio Grondona.
Gerardo Flores played only one match with Zacatepec, in a quarter final game of the Clausura 2004 season versus Club Leon.
Gerardo Flores played a single match for Cajeteros de Celaya in the Primera A's Apertura 2004 season.
During his stay Flores and his teammates helped Jaguares reach the Quarter Final of the Clausura 2009 playoffs losing versus Pachuca.
On December 16, 2015, it was made official that Flores would be joining Deportivo Toluca in a season-long loan deal from Cruz Azul.
In 2003, Flores was chosen by coach Julio Grondona to be part of the Mexican squad participating in the 2003 FIFA U-17 World Championship in Finland.