The club was founded in 1963 under name of Araz, re-established by Misir Abilov in 1995 and consisted of amateur footballers. Officially as a professional football club it was registered as Araz Football Club in 1997. Since 1998 the club is called Bakili Baku.
In May 2014, AFFA decided to ban the club from playing next season after players didn't appear at the last game of Azerbaijan First Division. In August 2014, AFFA overturned their decision by allowing club to participate in the 2014–15 season.