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The club was established in 1900. They made their first championship final in the 1930 season, where they met US Quillan, and defeated them 4 points to nil in Bordeaux, and thus capturing their first championship title. The club experienced some success in the coming years in the Challenge Yves du Manoir competition as well; winning it in the 1932 season and then becoming runners-up to Lyon OU in the 1933 season.

Agen would have another successful run in the 1940s, beginning with the 1943 season when they defeated Stade Bordelais 11 to 4 to win the Coupe de France. That season they also made it to the championship final; though they were defeated by Aviron Bayonnais 3 points to nil at Parc des Princes in Paris.

In 1945 they again won the title of the French championship, defeating FC Lourdes 7 points to 3 in the final in Paris. The championship was one of two titles that season, as Agen also won the Coupe de France, defeating Montferrand 14 to 13. Agen featured in one more championship that decade, losing to Toulouse 10 points to 3.

Agen were relatively quiet during the 1950s, though they again rose to prominence during the 1960s. In 1962 they again became of the champions of France after defeating Béziers 14 points to 11 in the season final. The following season they won the Challenge Yves du Manoir, defeating Brive 11 points to nil in the final. Agen became the French champions on two more occasions during the 1960s, defeating Brive in 1965 and then Dax in 1966.

The club had another successful run during the 1970s, starting with an unsuccessful Challenge Yves du Manoir final, losing to Toulon 25 points to 22. They were unsuccessful again in 1975 in the Challenge Yves du Manoir, losing to Béziers 16 points to 12 in the final. However they would then meet Béziers in the championship final of the 1976 season, and defeat them 13 to 10 to win their first championship since 1966.

Agen went through period of success in the 1980s after winning the championship in 1982, defeating Aviron Bayonnais 18 points to 9 in the final. The following season they won the Challenge Yves du Manoir as well after defeating Toulon 29 points to 7. In 1984 they again contested the championship final, though they eventually lost it to Béziers. They unsuccessfully contested it again in 1986, losing to Toulouse 16 to 6. They were also runners-up in the 1987 Challenge Yves du Manoir, losing to Grenoble. However, in 1988 they again won the championship, defeating Stadoceste Tarbais 9 to 3 in the final.

They contested the final again in the 1990 season, losing to Racing Club de France 22 points to 12. In 1992 they won the Challenge Yves du Manoir, defeating RC Narbonne 23 to 18.

Professional era

In 1998 they played in their first European cup final, the European Challenge Cup, losing to fellow French team US Colomiers 43 to 5 in the final. On June 8, 2002 they lost to Biarritz Olympique in the championship final.

In recent years, one of their biggest stars has been Fijian winger Rupeni Caucaunibuca. He led the team in tries in 2005 and 2006, and led Pro D2 in that category during Agen's most recent promotion season in 2010. However, he would be dismissed from the team in September 2010 after failing to report to the team for preseason workouts (several weeks later, he would reemerge at Toulouse).