Nicknamed Los Toros, the club was founded on 8 September 1962 after a merger of clubs Morazán, Interrogación and Juvenil and by initiative of Humberto Bermúdez, Evelio de León, Felipe Sánchez, José María Munguía, José Rivera, Vicente López and Feliciano Boj.

[1] Forty five years later, they earned their historic promotion to Liga Mayor by defeating Juventud Retalteca 3–0 (3–2 agg.)

This was also the first time in Primera División de Ascenso history that the same team won both the Apertura and Clausura tournaments, thus being automatically promoted without a need of an "extra" game.

[3] In the Apertura 2021, under Roberto Hernández, Malacateco claimed their biggest success in the club history by winning their first Liga Nacional title after defeating Comunicaciones 2-0 on 2 January 2022.

The Estadio Santa Lucía is the official venue of the team, it is located in the municipality of Malacatán in San Marcos, has a capacity for 7,000 spectators and also has synthetic grass and electric lighting.