The club's inception dates back to the early 1950s. Following the completion of the Agdam city stadium in 1951, serious efforts were made to establish the club as a professional sports organization. Initially competing under the name "Məhsul," Qarabag first participated in the Azerbaijan championship in 1966, finishing the championship in fourth place. Qarabağ competed in the national championship for four consecutive years.

During these years, the club's best result came in 1968 when it secured second place. However, after 1968, due to neglect, the team was absent from the national championships for a long time. In 1977, Qarabağ was revived under the name "Şəfəq" and competed in the second division of the Azerbaijan championship that same year. "Şəfəq" remained Agdam's sole football representative until 1982.

From 1982 to 1987, the club competed under the name "Kooperator." Qarabağ was first crowned champion of Azerbaijan in 1988, a title won while Azerbaijan was still part of the former USSR. After this championship, Qarabağ earned a spot in the second division of the USSR championship. In 1989, Qarabağ competed in the 9th zone of the USSR championship. In 1990, due to changes in the zone competitions of the USSR championship, Qarabağ had to participate in the zone competitions of the Azerbaijan championship.

In 1991, following the dissolution of the USSR, Azerbaijan organized its independent football championship. Qarabağ is one of the only clubs that have participated in all seasons since then. Certainly, the years following independence have been challenging for Qarabağ. After Agdam was occupied by Armenian forces in 1993, the team operated as a "refugee club." In 1993, our team won the Azerbaijan championship title and the national cup. Qarabağ was also awarded the Super Cup as the first in the history of Azerbaijani football to achieve a "Golden double." Additionally, the club suffered significant financial difficulties. As a result, from 1998 to 2001, it performed poorly in the premier division of the national championship. Furthermore, financial problems led to the departure of key players from Qarabağ.

All these problems were resolved after 2001 when one of the largest holding companies in Azerbaijan, "Azersun," took over the sponsorship of the team. Thanks to the generous support of "Azersun" Holding, significant efforts were made to keep Qarabag in the spotlight, not only in Azerbaijan but across the Eastern and Turkic worlds. Soon, with the personal assistance of the company's president Abdulbari Gozal, the team's financial problems were resolved. Former Qarabağ players who had moved to other clubs due to financial difficulties were brought back. From that period, the club was called "Qarabağ-Azersun." Naturally, the new sponsor's care also impacted the team's performance. In 2001, "Qarabağ-Azersun" finished 9th in the national championship, but preparations for the following season were underway, setting high goals. However, due to known incidents in Azerbaijani football, the 2001-2002 championship was suspended mid-season, preventing the achievement of these goals.

In 2003, several changes were made in the management structure of "Qarabag-Azersun," and Tahir Gozel was appointed as the vice-president of the team. Tahir Gozel's arrival marked a new chapter in Qarabağ's history. All resources were mobilized to achieve success in the national championship. As a result of these efforts, Qarabağ returned to the winners' circle in the 2003-2004 season, claiming the bronze medals of the championship. The club started the 2004-2005 season with higher ambitions. As part of these goals, leadership appointed the experienced coach Igor Ponomaryov, who resided in Sweden, as the head coach. Soon, the team recruited some of the leading football players in the country, many of whom were national team players. It's also worth noting that in 2004, at the initiative of Tahir Gozel, Qarabağ's historic name was restored, and the team was once again referred to by this name. Additionally, Tahir Gozel commissioned a new logo, designed in England, which depicted horses, the symbol of Qarabağ, adorned with various football attributes. In 2006, under the leadership of coach Boyukaga Agayev, our club won the national cup.

In August 2008, the club management appointed Gurban Gurbanov as the head coach. This move opened a new chapter in the history of Qarabağ. Gurban Gurbanov led the team to win the Azerbaijan Cup in his first season. In the 2009/10 and 2010/11 seasons, our team finished the championship with bronze medals. After starting the next season in fourth place, our team again claimed bronze in the 2012/13 season. In the 2013/14 season, Qarabağ's longing for a championship ended, as Gurban Gurbanov's players became the champions. From that championship onwards, Qarabağ retained the championship title in the 2014/15, 2015/16, 2016/17, and 2017/18, 2018/19, and 2019/20 seasons. In the 2014/15, 2015/16, and 2016/17 seasons, our team also won the Azerbaijan Cup, achieving a "Golden double" three times consecutively and writing a new chapter in history. After winning a silver medal in the 2020/21 season, our team won both the championship and the cup in the 2021/22 season. A year later, Qarabağ added a second star to its logo with its 10th gold medal.

Our team has made history in Azerbaijani football by qualifying for the group stages of UEFA's club tournaments ten times consecutively. Qarabağ participated in the Europa League eight times, the Champions League once, and the Conference League once. Our team made it through the group stage of the Conference League in the 2021/22 season, achieving another first in the history of Azerbaijani football. A year later, Qarabağ repeated the same success. In the 2023/24 season, another first was recorded when Qarabağ finished second in the group of the Europa League, becoming the first Azerbaijani team to advance to the playoffs of this tournament.

In the 2017/18 season, competing in the group stage of the Champions League, our team faced giant clubs such as Chelsea (England), Atletico (Madrid, Spain), and Roma (Italy), earning two points and making a name for itself worldwide.