The club was founded in the early 1950s. After the construction of Agdam city stadium was completed in 1951, serious work was done to form the club as a professional sports organization. "Garabagh", which performed under the name "Mahsul" for some time after its foundation, participated in the Azerbaijan championship for the first time in 1966. That year, the club finished the championship in 4th place. "Qarabag" fought in the national championship for 4 years in a row. His best result over the years was in 1968 when he finished 2nd. However, after 1968, due to neglect, the team was not represented in the national championships for a long time. In 1977, "Karabakh" was restored under the name "Shafaq". In the same year, "Shafaq" competed in the 2nd division of the Azerbaijan Championship. "Shafaq" became the sole representative of Agdam football until 1982. From 1982 to 1987, the club participated in competitions under the name "Cooperator". "Karabakh" was awarded the title of Azerbaijan champion for the first time in 1988. It should be noted that this championship was won when Azerbaijan was part of the former USSR. After that championship, "Karabakh" qualified for the 2nd division of the USSR Championship. In 1989, "Karabakh" competed in the 9th zone of the USSR Championship. In 1990, since changes were made in the zone competitions of the 2nd division of the USSR championship, "Karabakh" had to participate in the zone competitions of the Azerbaijan championship. In 1991, after the collapse of the USSR, the independent football championship of Azerbaijan was organized. "Qarabag" is one of the two clubs of Azerbaijan that has participated in all the seasons held so far. Of course, during the years of independence, "Karabakh" had many hard times. After the occupation of Aghdam by Armenians in 1993, the team operated as a "refugee club". In addition, the club was seriously suffering from financial difficulties. It is for this reason that in 1998-2001 he showed a poor result in the strong team of the national championship. Moreover, the financial situation led to the club's leading players leaving "Karabakh". All these problems were solved in 2001 after "Azersun", one of the largest holdings operating in Azerbaijan, sponsored the team. The "Azersun" Holding company, which gained a name not only in Azerbaijan, but also in the whole east and the Turkic world with its good deeds, started practical work in order not to forget "Karabakh". The team's financial problems were quickly solved with the direct personal help of the company's president, Abdulbari Qoozal. Former "Garabagh" players who moved to other clubs due to impossibility were returned to the team. From that period, the club was called "Karabagh-Azersun". Of course, the care of the new sponsor would affect the results of the team. In 2001, "Garabagh-Azersun" took the 9th place in the national championship, but preparations for the next season were going on seriously, and the club had the task of taking the highest places. However, it was not possible to achieve the goal as the championship in 2002-2003 was suspended in our country after the well-known events in Azerbaijani football. In 2003, a number of changes were made in the management structure of "Qarabag-Azersun" and Tahir Goozal was appointed the vice president of the team. After Tahir Goozal's arrival to the club, a new page has opened in the history of "Qarabag". All opportunities were mobilized for the team to succeed in the national championship. And it was the result of these efforts that in the 2002-2003 season, after a long break, "Garabagh" was again among the winners of the Azerbaijan championship and won the bronze medals of the championship. "Karabakh" wanted to start the 2004-2005 season more ambitiously. For this purpose, the management appointed our compatriot, experienced coach Igor Ponomaryov, who lives in Sweden, to the post of head coach. In a short time, the leading football players of the country were involved in the team. Most of them are football players who chase the ball in our national team. Let's note one more point that it was on the initiative of Tahir Goozal that in 2004 the historical name of "Qarabag" was returned to itself and the team started to be called by this name again. In addition, Mr. Tahir made a new logo for the club. Horses, symbols of "Karabakh", are depicted in this logo made by special designers in England. They are decorated with various attributes of football.
 
Our club won the national cup in 2006 under the head coach of Buyukaga Aghayev. 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 "Karabakh". Gurban Gurbanov won the Azerbaijan Cup in his first season. In the 2009/10 and 2010/11 seasons, our team finished the championship with bronze medals. In 2012/13, our team, which was 4th in the following season, won bronze again. In the 2013/14 season, our "Karabakh" longing for the championship ended, Gurban Gurbanov's team won gold medals. Starting with this championship he retained his championship title in the 2014/15, 2015/16, 2016/2017 and 2017/18 seasons. In 2014/15, 2015/16 and 2016/17, our team wrote a new history by winning the "golden double" 3 times in a row, as well as the championship and the Azerbaijan Cup. In the 2017/18, 2018/19, 2019/20 and 2021/22 seasons, our team won the title of Azerbaijan champion.
 
Our team made history in Azerbaijani football by qualifying for the group stages of UEFA club tournaments 9 times in a row. "Qarabag" participated 6 times in the European League, 1 time in the Champions League, and 1 time in the group stage of the Conference League. By passing the group stage of the Conference League in the 2021/22 season, our team achieved another first in the history of Azerbaijani football. In the 2022/23 season, our team, which started the competition from the Champions League, eventually progressed to the Conference League playoffs.
 
In the 2017/18 season, our team, which fought against giant clubs such as "Chelsea" (England), "Atletico" (Madrid, Spain) and "Roma" (Italy) in the group stage of the Champions League, scored 2 points in the group and made a name for itself in the world. "Garabagh" is not only the team that won the most points in the club rating for Azerbaijani football, but also the club that won the most victories and scored the most goals.