Founded in 1962, following the merger of Flacăra-Unirea Târgu Jiu and CIL Târgu-Jiu, Pandurii is one of the four Romanian clubs that represent the country at the European Club Association. Domestically, Gorjenii have never won any major honour, but finished as runners-up in the League at the end of the 2012–13 season and lost a League Cup final in 2015. They qualified for the very first time in a European competition in 2013, playing in the UEFA Europa League and reaching the group stage.
Pandurii Târgu Jiu was founded in August 1962, after the merger of the two big rivals from the town, Flacăra-Unirea Târgu Jiu and CIL Târgu-Jiu. The club entered the fourth division of Romanian football, with a strong objective, to promote immediately in the third division. And the target was reached, Pandurii gaining the promotion to Divizia C in June 1963. Their first game in this division was played on 1 September 1963, against Siderurgistul Hunedoara. Pandurii won by a big margin, 6–0, goals scored by Chițu (12'), Nelu Băloi (35'), Melinte (53', 80') and Vasilescu (83', 85').
In the first years, Pandurii finished constantly in the first half of the standings, so the club decided to attack a promotion to Divizia B. In the 1976–77 season, with a young team and with Titus Ozon as coach, the dream came true. Pandurii dominated the competition, climbed from the first stages on top of the standings and won the promotion to the second division. But this level was a much bigger hat to wear for Pandurii, who relegated the next season back to Divizia C.
The following years, the team changed frequently the division, promoting to Divizia B and relegating after a few years. They played in Divizia B between 1979–1983 then between 1986 and 1991. After a decade in Divizia C, in 2000 the team promoted again in the second league, and in 2004 finished second, behind Sportul Studențesc.
Beginning years in the top league (2005–2011)
Squad of Pandurii Târgu Jiu in November 2006
The performance from the last seasons was an incentive for the management who decided to push for the first presence of Pandurii in Divizia A. With Emil Săndoi as coach, and with a young group of players like Tiberiu Lung and Sorin Vintilescu but also with some experienced players like, Florin Popete, Robert Vancea and Romulus Buia, the team won the promotion.
It was difficult to maintain its position in Divizia A, and Pandurii finished their first season in the 15th place, right below the relegation line. But the Romanian Football Federation decided at the end of the season not to give Sportul Studențesc their licence for the following year, and kept instead the first team under the line, Pandurii. With the bullet dodged, the management decided to enforce the team, so the relegation shouldn't be a problem.
In the 2015–16, season of Liga I Pandurii had many achievements along the season with the same coach and players like UEFA Europa League winner Cristian Săpunaru, Dan Nistor, Ioan Hora and Mihai Răduț and Narcis Răducan as president. In April 2015 they became the first team to win a match in Liga I with the new play-off, play-out system. On February 6, 2016, they secured both a place in the competition play-offs and a place in a European competition next year with a victory with ASA 2013 Târgu Mureș. During this season they had the most matches without a defeat, about 10 games. At the end of the season, Pandurii finished on the podium as third-place qualifying for the second time in UEFA Europa League, but this time in the third qualifying round.