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1927–1993: Rise and fall

Football Club d'Annecy was founded in May 1927. The first president of the club was Louis Monnet, who held the office until 1933 when he was replaced by Jean Chatenoud. In the 1941–42 Coupe de France, with France divided into three zones during the German occupation of France, the team defeated Saint-Étienne 4–0 and Saint-Chamond 2–1 to reach the quarter-finals of the Zone libre section, where they lost 1–0 to Toulouse.

The club turned professional in 1942 after winning the Lyonnais Division Honneur, but was forced to return to its former status as amateur a year later as professional football clubs were outlawed. As amateurs, Annecy won the league twice more in 1946–47 and 1947–48 before joining the Championnat de France Amateur on its formation for 1948–49. Winning the Coupe de Lyonnais in 1953–54 was capped by finishing top of the Championnat's south-eastern section a year later. The team regained the Coupe de Lyonnais in 1958–59 and ended the 1959–60 campaign as the amateur champions of France. Chatenoud finally stepped down in 1970, after 37 years as president. The Championnat was dissolved after the 1970–71 season, and Annecy were subsequently accepted into the Division 3 Sud-Est.

During their first season in the new league, Annecy were nearly promoted, but lost a play-off match to Martigues. The team competed in the division until 1973–74, when Annecy were relegated back to the Lyonnais Division Honneur. The team revived during the early 1980s, achieving promotion to the fourth level for 1980–81 before winning the championship in 1983–84. Another promotion in 1987–88 saw the club in the second tier for 1988–89, and prompted a change back to professionalism. Annecy's best season that far came in 1990–91, when the team finished ninth in the league and reached the last 16 of the Coupe de France. However, on relegation in 1992–93, Annecy fell as swiftly as they had emerged – the club was wound up on 16 October 1993, and therefore gave up its professional status along with its place in the third level.

1993–: Rebirth and rise

Annecy Football Club was formed on the same day as FC Annecy's demise, and took up a league place five tiers below that of the former team in the Rhône-Alpes Promotion Honneur Régional. The new club was promoted in its second season, and repeated this feat two years later. After nine years at the sixth level, the Rhône-Alpes Honneur Ligue, Annecy were relegated again in 2007–08. In 2013 the club regained the historic name FC Annecy, and in 2015 won the Rhône-Alpes Division Honneur, to gain access to the Championat de France Amateur 2. In 2016 the club were again promoted to the Championnat de France Amateur.

Annecy were in top place in Group D of the 2019–20 Championnat National 2 by two points when the season was prematurely ended due to the COVID-19 pandemic, and were therefore promoted to Championnat National.

In March 2021, Annecy were fined by the FFF for coaching irregularities. The club had been coached by Rémi Dru since the dismissal of Michael Poinsignon in December 2020, and in January 2021 had employed Jean-Yves Chay with the title of head coach. The FFF found that Rémi Dru was in fact performing the function of head coach, and fined the club €3,000 per match played under these circumstances.

On 13 May 2022, Annecy beat Sedan 2–0, securing promotion to Ligue 2 as Championnat National runner-up under Laurent Guyot; it was their first time in the second tier in 29 years, and the first since the division became one nationwide group. In the 2022–23 Coupe de France, the team reached the quarter-finals for the first time since 1942 after winning on penalties following a 1–1 draw at Paris FC, and then made the semi-finals by winning the same way after a 2–2 draw at Marseille.

On 3 August 2023, Annecy were originally relegated to Championnat National but were reprieved by the ruling of a French court due to Sochaux’s administrative relegation to the third tier of French football.