Founded in 2005 as a merger between CD Tres Cantos Balompié and CD Embarcaciones, Tres Cantos achieved immediate promotion to Primera Regional in its first season. In 2008, after a fusion with CD La Paz, the club achieved an administrative promotion to Regional Preferente.[2]
Tres Cantos achieved promotion to Tercera División in June 2017, after finishing third in the regular season.[3] On 4 July of the following year, the club became CF Rayo Majadahonda's reserve team, after an agreement between both sides was reached.[4]
In April 2020, after Rayo Majadahonda announced an affiliation with CD Paracuellos Antamira (formerly Alcobendas Sport), the agreement with Tres Cantos was cancelled.[5]