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FC Versailles was formed in 1989 as the result of a merger between Racing Club Versailles and Companion Sports Versailles. The new club took Racing Club Versailles' place in Division 3 and were placed in the North section. FC Versailles' first season was not successful as they finished 14th, amassing 24 points from 30 matches, and were relegated from the division. Competing in Division 4, they achieved two successive eighth-placed finishes before a sixth-placed finish in the 1992–93 season. In the summer of 1993, Versailles were one of the clubs accepted into the newly formed National 3. They ended the season with 40 points, finishing as runners-up behind Le Mans B.

Versailles struggled in the National 2 and were relegated after one season after finishing 17th in the table. The team returned to the National 3 and achieved a couple of mid-table positions in the following two seasons. Versailles qualified for the Championnat de France Amateur 2 Group B in the 1997–98 campaign and finished 13th in their inaugural season. The following year, Versailles were moved to Group H and the side finished 15th out of 16 teams in the division, thereby suffering relegation to the Division d'Honneur Paris Île-de-France. Versailles remained in the same division for the next six seasons, achieving a highest finish of third place in the 2000–01 campaign. In the 2004–05 season the team again suffered relegation after finishing bottom of the division with 46 points from 26 matches. Versailles have played in the DSR Paris Île-de-France since the 2005–06 season. In the 2009–10 campaign, Versailles reached the Ninth Round of the Coupe de France before losing to Beauvais. Versailles caused an upset by defeating Ligue 2 club Dijon in the Eighth Round.

On 29 January 2022, Versailles eliminated Ligue 2 side Toulouse in the round of 16 of the Coupe de France following a 1–0 win, and went on to qualify for the semi-finals after beating Bergerac in a penalty shoot-out. Versailles was eventually defeated 2–0 by Nice in the semi-finals. Later in the 2021–22 season, Versailles secured promotion to the Championnat National.