The team was in the first division of El Salvador from 1987 on for several years.

Cojutepeque was a runner-up in the 1988–89 season, losing on penalties to L.A. Firpo in the finals after the game ended 2–2 after extra time.

Cojutepeque's first trophy was the Liga Ascensio, which they won in 1986-1987.

Cojutepeque's honours include the following: Players with senior international caps

This article about a Salvadoran football club is a stub.