On 23 July 1930, in the café Norat in La Rambla of Girona, Girona Futbol Club was founded upon the dissolution of Unió Esportiva Girona for economic reasons. The team subsequently entered in the second division of the Catalan Championships. Its first official match was against Colònia Artigas with the lineup: Florenza, Teixidor, Farró, Flavià, Comas, Corradi, Ferrer, Escuder, Clara, Torrellas and Taradellas.
1935–36 was the first season Girona played in Segunda División, and the club finished in top position in its group, subsequently appearing in the playoff stage against Celta de Vigo, Real Zaragoza, Arenas Club, Real Murcia and Xerez, but finishing second from bottom, thus out of the La Liga promotion zone.
After the Spanish Civil War, the club fluctuated between the second level and Tercera División, falling into the latter category in 1959 and being further demoted in 1980 – Segunda División B was created as the new division three in 1977, and the club lasted three years in the competition. In 1968, construction of the Estadi Montilivi began, with home matches being held there on a permanent basis from 1970 onwards after nearly five decades at the Vista Alegre stadium.
In the following decades, Girona alternated between the third and the fourth divisions, even spending three seasons in the regional championships, in 1982–83 and 1997–99. On 16 June 2008, after defeating Ceuta 1–0 in the play-offs, the Raül Agné-led side achieved a second consecutive promotion, returning to the second tier after a 49-year absence.
On 22 July 2010, a group of local businessmen led by Ramon Vilaró, Joaquim Boadas and Josep Slim purchased 72% of the club's shares, previously held by former club president Josep Gusó and Josep Rofes, thus becoming the new owners of Girona. Vilaró was elected the new president while Agné, after a spell with Recreativo de Huelva, returned as manager for the upcoming second division campaign, lasting in the position until 14 January 2012 when he was sacked following a 0–3 loss at Recreativo.
In 2011, Girona created a reserve team, having previously grown a natural grass pitch in Palau. On 9 May 2013, the club's board of directors, under the slogan "El Girona FC també és meu" ("Girona FC is mine too"), approved an increase of the club's capital in €300,000 to be distributed in €10 shares, aiming to balance its estate.
On the last matchday of the 2014–15 season, Girona needed to beat Lugo at home to earn promotion to La Liga, but were denied by a last-minute goal by the visitors. Girona had to settle for a play-off place, but were eliminated in the semi-finals by Real Zaragoza, despite winning the first leg 3–0. The next season, they reached the play-off final but were defeated by Osasuna. Girona finally earned promotion to La Liga after the 2016–17 season as they finished runners-up to Levante. This was the first time that Girona had ever been promoted to La Liga in their 87 year history.
On 23 August 2017, it was announced (CFG) had purchased 44.3% ownership in Girona. Another 44.3% was held by Girona Football Group, led by Pere Guardiola, the brother of CFG-owned Manchester City manager Pep Guardiola. On 29 October 2017, Girona recorded a memorable victory defeating reigning European Cup winners Real Madrid 2–1.
In July 2018 it was announced that Girona FC would be participating in their first ever Pre-Season international tournament held in India by
Nippon Toyota. Girona FC faced the Indian team Kerala Blasters and the Australian Team Melbourne City FC.