San Sebastián is one among many club out of the state of Guanajuato that have played in the Primera División de México.

[1] The club played its first official game on August 19, 1945 in the league tournament which they lost 1-0 to Monterrey.

The club did not fare well in its first year, in the 19 round, for example, San Sebastián was defeated 9-2 by Atlante.

San Sebastián came close to promotion in 1952, when they finished runner-up to La Piedad, and once again in 1954 when they again fell short, this time to Irapuato.

Due to the poor play and lack of supporters the club was disbanded in 1959.