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 for the 2019–20 season.[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]