The club was founded under the name of Goy Gol on 3 July 1995, based in Goy Gol. On 1 September 2005, Goy Gol was registered in Gabala by the Ministry of Justice, before the AFFA registered the team as professional on 5 September of the same year. In the summer of 2006, the team moved from Goygol to Qabala, before the club changed its name to Gabala on August 31, 2007.
On 10 May 2010, former Arsenal defender Tony Adams was appointed as new manager after signing £1 million per year deal with the club. In his first season in charge Gabala finished at 7th place in Azerbaijan Premier League. In November 2011, Adams resigned from being Gabala's coach due to family problems.
Despite the appointment of managers like Fatih Kavlak and Ramiz Mammadov, the club couldn't reach a satisfactory position in the league and was struggling in the middle of the table for many years. On 29 May 2013, Yuri Semin was appointed as new manager after signing £1 million per year deal with the club. In same year, the club qualified for European cups for first time in their history but lost to Neftchi Baku on penalties in final of Azerbaijan Cup.
In the 2015-16 season of Europa League they became the 3rd club from Azerbaijan to qualify for the group stage after Qarabag and Neftçi Baku. They eliminated Dinamo Tbilisi, Čukarički, Apollon Limassol and surprisingly Panathinaikos. They came 4th in their tough group of Borussia Dortmund, PAOK and FC Krasnodar. They managed to get two points both from 0-0 draws against PAOK.
As of 2007, predominantly due to UEFA requirements, the club proposed an extensive renovation of the stadium, which has since been in constant process of redevelopment. AFL Architects were appointed to design a new 15,000 capacity stadium and training facility in December 2008 after winning a limited design competition. Accommodation within the stadium will include hotel and conferencing facilities, as well as retail and corporate hospitality space, and a dramatic viewing deck at the top of the entrance tower. It is expected that the stadium was scheduled to open in 2014.
Gabala has a large fanbase in relation to its comparative lack of success on the pitch. Gabala's fan base has fluctuated over the years with high crowds coinciding with the club's success in the Premier League so that the club now averages in the top four best home attendances in the country.
Azerbaijani teams are limited to nine players without Azerbaijani citizenship. The squad list includes only the principal nationality of each player; several non-European players on the squad have dual citizenship with an EU country.
Lists of the players with the most caps, and goals for Gabala as of match played 14 February 2016 (players in bold signifies current Gabala player). Dodô is Gabala's most capped player, earning his 150th appearance for the club in their 7-0 victory over Mil-Muğan in the Azerbaijan Cup on 3 December 2015.