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.
Eibar was relegated to the third division at the end of the 2005–06 campaign. However, it won its group the next season, thereby qualifying for the promotion play-offs where it won its semi-final tie against Hospitalet 2–0 and defeated Rayo Vallecano 2–1 on aggregate in the decisive round, sealing its return after just one year. Eibar finished 21st in the 2008–09 season meaning they were related to the Segunda Division B.
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. Simultaneously, however, the club was threatened with relegation back to division three due to its financial inability to transform, as required by law, into a Sociedad Anónima Deportiva. In order to become a S.A.D. Eibar needed 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 CF were sent to the second tier as punishment for financial mismanagement, and Eibar were reinstated.