Founded in 2005 as a merger between CD Tres Cantos Balompié and CD Embarcaciones, Tres Cantos achieved immediate promotion to Primera Categoría in its first season. In 2008, after a fusion with CD La Paz, the club achieved an administrative promotion to Preferente Autonómica.[1]
Tres Cantos achieved promotion to Tercera División in June 2017, after finishing third in the regular season.[2] On 4 July of the following year, the club became CF Rayo Majadahonda's reserve team, after an agreement between both sides was reached.[3]