Founded in 1971, it currently plays in Primera Federación, holding home matches at the Municipal de Santo Domingo, with a 5,100-seat capacity.

After disposing of Sant Andreu and Alcoyano, the club was ousted by Real Unión of Irun in the final round with a 3–1 aggregate scoreline.

On 27 October 2009, Alcorcón secured the most famous victory in its history after it defeated La Liga powerhouse Real Madrid 4–0 at home in the first leg of its round-of-32 match in the Copa del Rey.

[5] In the club's first ever official match against a team from the top flight, its opponent fielded nine international players in its starting eleven: Jerzy Dudek, Álvaro Arbeloa, Raúl Albiol, Christoph Metzelder, Royston Drenthe, Mahamadou Diarra, Guti, Esteban Granero, Raúl, Rafael van der Vaart and Karim Benzema, with Ruud van Nistelrooy, Fernando Gago and Marcelo appearing as substitutes in the second-half.

In 2017, Alcorcón qualified to the Copa del Rey quarter-finals for the first time in their history after a penalty shoot-out victory over Espanyol, but were beaten 2–0 on aggregate by Alavés.