Gandzasar Football Club NGO was first established back in 1963, under the name Lernagorts FC, making it one of the oldest active football clubs in Armenian football. Based in the town of Kapan, the team have spent much of their history in the country's lower divisions, but have occasionally competed for major honours. The club have undergone a number of name changes, operating as FC Syunik Kapan, Kapan-81 FC and reverting back to Lernagorts FC, before adopting their current name in 2004.
Upon foundation, Gandzasar enjoyed instant success, as they lifted the SSR Armenia Cup in their inaugural year. During Armenia's time as part of the Soviet Union, Gandzasar competed in the SSR Armenia League, where they also found notable success. Indeed, they were crowned as league champions in both the 1989 and 1991 seasons. After Armenian independence, the side became a charter member of the new Armenian Premier League.
In their first season in the division, in 1992, the club finished in 6th place. However, they withdrew ahead of the 1993 campaign and have since spent much of their time in the lower tiers, failing to fully establish themselves as a top flight team. Recent seasons have seen the club begin to compete for major honours once again and the team have secured top-3 finishes in the league on three occasions, in 2008, 2011 and 2012-13, marking their best performances in the division so far. On each of those occasions, the team qualified for the following year's UEFA Europa League competition.
Alexander Petrosyan and Diego Lomba rank amongst the most notable players to have represented the team in the Premier League era. Both were prolific goalscorers for the side.
The team's home matches are played at Gandzasar Stadium, which opened in 1963 under the name Lernagorts Stadium. The venue became official club property in 2008 and subsequently underwent a major renovations process. It is currently able to hold up to 3,500 people.