Cobras was founded on 12 May 1980 as Cobras Querétaro, which was owned by television company Televisa. In 1985, the club acted as Club América's reserve team, while also pitching its veterans. Also in that year, it was first promoted to the top division after beating C.F. Pachuca with a score of 3–1. The stay would be however short-lived, as the team was immediately relegated, after collecting 31 points in 40 matches.
After Cobra's relegation, Alejandra de La Vega bought the club and moved it to Ciudad Juárez, meeting immediate success as it reached the Liga de Ascenso final that year and beat Club León 1–0, in a game played at Estadio Azteca on 12 July 1988, with Joaquín Mendoza as manager.
In 1994, after the readjustments made in Primera División, Cobras folded, not being able to cope with serious economic problems. Seven years later, again as a feeder club - now to C.F. Monterrey - it was re-formed, playing and losing the 2003 promotion playoffs final, to Dorados de Culiacán.
- 1985–86, 1987–88
- Runner-up (1): 2002–03
- Mexican Cup: 1
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