Racing Club San José was founded in 1939, being renamed to Club Deportivo San José in 1943 and to Unión Deportiva Amistad in 1948. Amistad later became a farm team of Real Zaragoza, and the club decided to create Real Zaragoza Club Deportivo Aficionados in 1958, to serve as a second reserve team behind Amistad. The latter club achieved promotion to Tercera División in their first season, being later renamed to Juventud Club de Fútbol, as no reserve teams could compete in a national division with the same name of their parent club.
Despite reaching the promotion play-offs in 1962, where they lost to Alcoyano, the club spent the following two seasons unregistered. In 1964, after Amistad was dissolved, Juventud took their place in the third division, being now named Club Deportivo Aragón.
Deportivo Aragón was renamed to Aragón Club de Fútbol in 1966, and played four seasons under that name before changing it to Deportivo Aragón. The club enjoyed their best years under that denomination, as they played eight seasons in Segunda División B, and achieved promotion to Segunda División in 1985.
In 1991, after a change in the RFEF general regulations, Deportivo Aragón was dissolved for an official reserve team to take their place, named Real Zaragoza Club Deportivo "B". In 2011, after five seasons in Tercera División, the club bought a place in Segunda División B, but suffered relegation back to the fourth tier in 2013.
In December 2013, Zaragoza B returned to their previous name of Deportivo Aragón (officially Real Zaragoza Deportivo Aragón). In the 2016–17 season the club won Tercera División, Group 17 and promoted to the Segunda División B.[2]