Deportes Tolima was founded by Manuel Rubio Chávez in the year 1954 when he gave Juan Barbieri (an Argentinian living in Ibagué, Colombia) a sum of $5.000 Colombian pesos in order to hire soccer players from his native country, Argentina. Barbieri went back to Colombia with players such as Jorge Gandulfo, José Jamardo and Enrique Laino. With those players and some others Argentines and Colombians, Deportes Tolima competed for the first time in the Colombian football league in 1955 using the uniform of Racing Club de Avellaneda of Argentina. Deportes Tolima finished 7th in the league competing with 9 other teams.
2006 was a great year for Deportes Tolima, the team was second on the reclasificacion (overall points in the year), was the team with the most goals scored in the year, over 80, and were runners up in the Copa Mustang II. At the beginning of 2006 Deportes Tolima did not seem like a very strong team for the season as it did not sign any players. The coach was Jorge Luis Bernal who had been the coach for the reserve team for many years. Deportes Tolima played amazing both home and away games which included victories against Envigado 7–3, Nacional 5–1, and Millonarios 3–0. They reached the semifinals of the Copa Mustang I and was placed in a Group with Deportivo Pereira, Deportivo Cali, and Once Caldas but did not made it into the finals. The Copa Mustang II was even better than the first one. Tolima ended first in the league, and played the semifinals against Nacional, Pasto, and Chico. Nacional were leaders of the Group for most of the time while Deportes Tolima remained a point behind. A dramatic 2–1 away win over Nacional made them leaders, they advanced the final against Cúcuta Deportivo after a 2–0 win over Chico. The first game was away and Tolima lost 1–0 then in Ibagué the game ended tied 1–1 with Yulián Anchico scoring Tolima's goal.
For the 2007 season Deportes Tolima signed very important players like Nicolas Ahyr, Diego Cochas, Gustavo Savoia, Gustavo Bolivar, Leiner Rolong, Jorge Perlaza, Hernando Patino, Roller Cambindo, Javier Arizala, Bramhan Sinisterra, Ricardo Alvarez, and Haider Arboleda. With new coach Jaime de la Pava started competing in the Copa Libertadores and the Copa Mustang. In the Copa Libertadores Tolima defeated Deportivo Táchira in 2 games, that way Tolima entered to the group of Gremio, Cerro Porteño and curiously Cúcuta.