SD Ejea was founded on October 3, 1927 by the merging of Setia Foot-ball Club, Numancia Foot-ball Club and Sporting Foot-ball Club.[2] Higinio Villacampa Murillo became its first president.[3]
After competing in all categories of Aragonese regional football, Ejea was for the first time promoted to the Tercera División in 1956-57 season, also reaching the final of the Aragon Championship of Fans.[4]
After a first season in the third division where the club successfully avoided relegation, on 27 June 2019, Ejea agreed collaboration terms with SD Huesca to become their reserve team.[5] On 25 June, 2019 Javi Suárez was appointed the new head coach.[6] He substituted Guillermo Fernández Romo, who saved the club in Segunda División B in its debut season in the league.[7]