Deportivo Garcilaso was founded on 13 April 1957 as Deportivo Lucre by the Garmendia brothers. It was then sold to a church pastor, Monsignor Publio B. Prada Torres, who promoted football at the Great Inca Garcilaso de la Vega school and was a father in the church of San Blast.

In 1970 Deportivo Garcilaso was invited by the Peruvian Football Association to participate in the Copa Presidente de la República. After overcoming the group stage, they were eliminated by Porvenir Miraflores

The club has participated on several occasions in the final stages of the Copa Perú, one of its best campaigns being the 1979 Copa Perú where it reached the Hexagonal Final. They were departmental champion after defeating Manco II of Quillabamba in the final and qualified for the Regional Stage where they eliminated América Star de Juliaca and Juventud La Joya de Puerto Maldonado. In the National Stage, they knocked out Pesca Peru de Mollendo in their group and qualified together with Deportivo Centenario de Ayacucho to the final. In that phase they finished in third place, tied with Defensor Lima, behind ADT Tarma and Comercial Aguas Verdes de Zarumilla, and were eliminated from the tournament.

In the 2000 Copa Perú, the club qualified to the National Stage, but was eliminated by Coronel Bolognesi in the Quarterfinals. In the 2003 Copa Perú, the club qualified to the National Stage, but was eliminated by Deportivo Enersur in the Quarterfinals. In the 2007 Copa Perú, the club qualified to the National Stage, but was eliminated by Unión Minas in the Round of 16.