Founded on 25 September 1937, and joining the professional league in 1949, Boca Juniors de Cali was one of the most important teams of the El Dorado era, rivalling with clubs such as Millonarios from Bogotá and crosstown rivals América de Cali. Boca Juniors placed as runners-up in the 1951 and 1952 seasons, finishing behind Millonarios in both cases and third in the following season, behind Millonarios and Atlético Quindío. After those three campaigns, and although the team's performance started dwindling, it was able to stabilize in the middle of the table. During this period, the club also won the Copa Colombia in the 1950–51 and 1951–52 seasons. In the 1952–53 season, they finished as runners-up in that competition, once again behind Millonarios. In 1958, Boca Juniors de Cali did not take part in the professional league. The club suffered the economic crisis that engulfed several Colombian clubs after El Dorado, and the lack of sponsorships, fanbase, and income caused the club to withdraw, leading to its disbanding and making way for the return of Deportivo Cali, who bought their membership in the professional league and along with América went on to become the city's most representative clubs.
In 1987, a group of football executives led by Hernando Ángel refounded Boca Juniors as an amateur club and football academy taking part in the tournaments of the Valle del Cauca regional league. It has also participated in the youth tournaments organized by the FCF and has built an important reputation due to its success in different tournaments and the number of players it promotes to professional football. Several well-known players such as Giovanni Hernández, Wilman Conde, Hugo Rodallega and others have emerged from its ranks. Owing to Ángel also owning both Deportes Quindío and Universitario Popayán, the latter clubs became a platform for the Boca Juniors players to access professional football, being first promoted to Universitario and then to Deportes Quindío. On 12 March 2019, the General Assembly of Dimayor approved a proposal to relocate Universitario Popayán from Popayán to Cali starting from the second half of the 2019 season, with the aforementioned club being rebranded as Boca Juniors. This move allowed the return of Boca Juniors to professional football after 61 years.
