Cortuluá was founded in 1967 by a group of people headed by Paraguayan former player and coach Hernando Acosta, and entered Categoría Primera B for its first season in 1991.

In 2006, the United States Treasury identified the football club as one of ten businesses allegedly operating on behalf of one of the most wanted Colombian drug barons, Carlos Alberto Renteria Mantilla.

Cortuluá qualified for the final of the "Torneo Apertura", surpassing Deportes Palmira, Deportivo Rionegro, and Atlético Bucaramanga in Group A of the semi-finals.

They came on top of Group B, ahead of Unión Magdalena, pre-tournament favorites América de Cali, and Deportivo Pereira and thus earned promotion for the 2015 season.

[5] After four years in the second tier, Cortuluá were able to return to Primera A at the end of the 2021 season, winning their semi-final group to clinch one of the two promotion spots.

[7] Following the team's relegation from Primera A, the club's owner Ignacio Martán announced his intention to move Cortuluá out of its hometown, citing the lack of financial support from successive local administrations.

On 14 December 2022 the General Assembly of DIMAYOR approved Cortuluá's proposal to move their home matches from Tuluá to Yumbo, Valle del Cauca Department, starting from 2023.