The club was founded in the early 1950s. After the construction of the Aghdam city stadium was completed in 1951, serious work was done to form the club as a professional sports organization. After its establishment, “Qarabag”, which played under the name “Mahsul” for a while, participated in the Azerbaijan championship for the first time in 1966. That year, the club finished the championship in 4th place. “Qarabag” competed in the national championship for 4 consecutive years.

The best result during these years was achieved by taking 2nd place in 1968. However, after 1968, due to neglect, the team was not represented in the national championships for a long time. In 1977, “Qarabag” was restored under the name “Shafaq”. In the same year, “Shafaq” competed in the 2nd division of the Azerbaijan championship. “Shafaq” was the only representative of Aghdam football until 1982.

From 1982 to 1987, the club participated in competitions under the name “Kooperator”. “Qarabag” was awarded the title of champion of Azerbaijan for the first time in 1988. It should be noted that this The championship was won when Azerbaijan was still part of the former USSR. After that championship, “Qarabag” qualified for the 2nd division of the USSR championship. In 1989, “Qarabag” competed in the 9th zone of the USSR championship. In 1990, changes were made to the zonal competitions of the 2nd division of the USSR championship, so “Qarabag” was forced to participate in the zonal competitions of the Azerbaijan championship.

In 1991, after the collapse of the USSR, an independent football championship of Azerbaijan was organized. “Qarabag” is one of the only clubs in Azerbaijan that has participated in all seasons held so far. Of course, “Qarabag” had many difficult days during the years of independence. After the occupation of the city of Agdam by Armenians in 1993, the team operated as a “refugee club”. In 1993, our team won the title of Azerbaijan champion and the national cup. “Qarabag” was also awarded the Super Cup as the author of the first “Golden Double” in the history of national football. was made. Of course, in addition to this, the club was also seriously suffering from financial difficulties. For this reason, it showed poor results in the strong group of the national championship in 1998-2001. Moreover, the financial situation led to the club's leading footballers leaving "Qarabag".

All these problems were solved in 2001 after one of the largest holdings operating in Azerbaijan, "Azersun", took over the team as a sponsor. "Azersun" Holding Company, which has gained a name not only in Azerbaijan, but also in the entire East and the Turkic world with its good deeds, began practical work to ensure that "Qarabag" was not forgotten. Soon, with the direct personal assistance of the company's president, Abdulbari Goozal, the team's financial problems were resolved. Former "Qarabag" players who had left for other clubs due to impossibility were returned to the squad. From that time on, the club was called "Qarabag-Azersun". Naturally, the care of the new sponsor would also affect the team's results. In 2001 Although “Qarabag-Azersun” took 9th place in the national championship, preparations for the upcoming season were in full swing and the club was tasked with taking the highest places. However, after the well-known events that took place in Azerbaijani football, the championship was suspended in 2001-2002 in our country, so it was not possible to achieve the set goal.

In 2003, a number of changes were made to the management structure of “Qarabag-Azersun” and Tahir Gozel was appointed vice-president of the team. After Tahir Gozel’s arrival at the club, a new page was opened in the history of “Qarabag”. All opportunities were mobilized for the team to succeed in the national championship. And it was precisely as a result of these efforts that in the 2003-2004 season, “Qarabag” again took part in the winners of the Azerbaijani championship after a long break and won the bronze medals of the championship. “Qarabag” intended to start the 2004-2005 season more ambitiously. For this purpose, the management went to Sweden Our compatriot, an experienced coach, Igor Ponomarev, who lives in the city, was appointed as the head coach. In a short time, the country's leading football players were attracted to the team. Among them, the majority of football players in our national team are players who play for the national team. Let's also note that it was on the initiative of Tahir Gozel that in 2004, the historical name of "Qarabag" was returned to itself and the team began to be called by this name again. In addition, Tahir bey had a new logo prepared for the club. This logo, prepared by special designers in England, depicts horses, the symbol of "Qarabag". They are decorated with various football attributes. Our club won the national cup in 2006 under the head coach of Boyukaga Agayev.

In August 2008, the club management brought Gurban Gurbanov to the post of head coach. This step of the club management opened a new page in the history of our "Qarabag". Gurban Gurbanov became the winner of the Azerbaijan Cup in his first season. In the 2009/10 and 2010/11 seasons, our team finished the championship with bronze medals. The following season, the team finished in 4th place.