Formed by the merger of Deportivo Gallo and Unión Deportiva Eibarresa, the club was originally known as Eibar Fútbol Club, before changing to Sociedad Deportiva Eibar. Originally an irregular team, it was not until the 1943–44 season that it was reorganised into a more full-time unit.
In 2013–14 Eibar earned, for the first time in its history, one of two direct promotion berths to La Liga, which was certified on 25 May 2014 with a 1–0 home win against Deportivo Alavés. (they celebrated their feat with confetti originally produced by Barcelona, who wear the same colours and had anticipated winning the Spanish league title, but that did not come to pass). Simultaneously, however, the club was threatened with relegation back to division three due to the financial inability of the S.A.D. to have a share capital of at least €2,146,525.95 before 6 August 2014. The club launched a campaign named Defiende al Eibar (Defend Eibar) with the aim of reaching the required share capital through a seasoned equity offering. On 15 July 2014 the club announced it had reached the established goal.
Eibar finished its first top-flight season in 18th, ending in relegation. However, after the season ended, 13th-placed Elche were sent to the second tier as punishment for financial mismanagement, and Eibar were reinstated.