Club Atlas was founded in a bar of Guadalajara, Mexico, where a few friends recalled their football experience at the Ampleforth College where they had spent the last few years. Alfonso and Juan José "Lico" Cortina, Pedro "Perico" and Carlos Fernández del Valle, the three Orendain brothers and Federico Collignon (who had studied in Berlin) finally decided in 1916 to set up a football team called "Club Atlas" and founded it in Guadalajara.

The technical ability that the "Atlistas" employed – triangular passing and skillful dribbling to avoid opponents' tackles – was impressive and they quickly joined the elite in Mexican football. As a result, Atlas and Chivas, a fellow Guadalajara team, have a long history in the first division and the game between them is called the 'Clásico Tapatío'.

Club Atlas had a golden age in the late 1990s under the management of Ricardo La Volpe, with promising players such as Rafael Márquez, Daniel Osorno, Juan Pablo Rodriguez, Pavel Pardo, Mario Méndez, Omar Briceño, Miguel Zepeda, and Cesar Andrade, but even though they had a team with enormous talent and reached the Verano 1999 final, they couldn't conquer the title and lost against Deportivo Toluca FC in a match defined by penalties.