[2][3] The club in its current form was established on August 1926 by Fazlli Frashëri, known as Sportklub Korça, later changing its name to Skënderbeu Korçë, after Albania's national hero Skanderbeg.

The first football club in the city of Korçë was formed on 15 April 1909 under the name Vllazëria by politician and poet Hilë Mosi.

These teams were local, however, and would only compete with one another, as the main football club to represent the city was Skënderbeu who overcome several problems at the start, some of which were even political.

[8] The championship winning side was: Klani Marjani, Kristaq Bimbli, Andrea Çani, Andon Miti, Lefter Petra, Fori Stasa, Nexhat Dishnica, Tomor Ypi, Thoma Vangjeli, Servet Teufik Agaj, Enver Kulla, Vasil Trebicka, Stavri Kondili, Aristotel Samsuri, with Qemal Omari as their manager.

The following year, Skënderbeu strongly fought to retain their title, but only finished as runners-up once again to KF Tirana, with Samsuri being the club's top goalscorer that season with seven goals.

In the next two championships held prior to World War II, Skënderbeu finished in fourth place in both years under manager Qemal Omari.

The majority of the players who were active in the 1930s were no longer playing football competitively, so the squad was virtually new, except for Klani Marjani, Bellovoda and Saro.

Manager Tato Bimbli decided to bring in young players in order to revive the squad during the 1947 season, when the club also changed its name to Dinamo Korçë for the Communist Party, Bimbli's decision to bring in young players paid off as the club finished third in the league out of nine teams.

During the winter of 2009–10, the club was bottom of the league and facing the real possibility of relegation from the Albanian Superliga, but there were seismic changes in terms of the ownership and the board, as a new president in the shape of Red Bull Albania CEO Agim Zeqo was appointed.

A new 16-member board was also elected, and a host of new donors attached themselves to the club, including some of Albania's most successful businessmen, such as Samir Mane, Irfan Hysenbelliu and Grigor Joti.

Journalist Blendi Fevziu was also named as a donor, alongside national Minister of Finance Ridvan Bode and the prefect of Korçë, Niko Peleshi.

[9] In order to escape relegation, the club brought in Mirel Josa as new head coach, along with a host of new players, both from Albania and neighbouring countries.

[10] Ahead of the 2010–11 season, the squad was revamped and under the guidance of Shkëlqim Muça as the head coach, new players were brought in, many of whom were Albanian internationals including Orges Shehi, Ditmar Bicaj, Endrit Vrapi, Jetmir Sefa, and Bledi Shkëmbi who was named captain following his return to his hometown club.

They were defeated by KF Tirana in their first ever Albanian Supercup game, and they spent much of the season in second place in the league, behind pacesetters Flamurtari Vlorë.

Shkëlqim Muça was replaced by Shpëtim Duro as head coach in February and defeated Flamurtari Vlorë in his first game in charge to move closer to top spot, and he went on to guide the club to 11 wins in his 13 games in charge, to win the Albanian title for the first time since 1933 and to qualify for the UEFA Champions League qualifying round for the first time in their history.

"[12] The club made its Champions League debut against Cypriot side APOEL in the second qualifying round on 13 July 2011, and they lost 2–0 at home, before losing 4–0 away as they were knocked out of the competition.

He guided the club to a 14 match unbeaten run to reach the top of the table, and he only lost two games in charge as they narrowly beat Teuta Durrës to the title with only a single point between the sides to claim the only Champions League spot once again.

They dropped into the UEFA Europa League play-offs, making their debut in the second most important continental competition with a 0–1 loss to Ukrainian side Chornomorets Odesa in the away leg.

In the championship, they began with a 1–0 victory over Besa Kavajë, then lost important matches against Flamutari and Kukësi, but recovered and claimed a winter lead place.

The summer transfer window was marked by the signing of the Albanian international Hamdi Salihi, who played at Rapid Wien.

They beat Milsami 2–0 both home and away to become the only Albanian side to qualify to the UEFA Champions League play-offs, where they met Dinamo Zagreb.

Their worst defeat in the European competition yet came the next matchday, a storming 1–5 loss to Sporting in the away leg at Lisbon, but also had the Albanian side scoring their first goal in the UEFA Europa League group stages.

They received 2 scoreless loses in the remaining matches respectively 2–0 away against Beşiktaş and 0–3 home against Lokomotiv Moscow to end the European campaign eliminating from group stage ranked in the last place.

The return match in Elbasan Arena saw Skënderbeu winning the regular time 2–1, while the extra periods yielded no further goals.

In September 2013 prior to an away game in Tirana the Ujqërit e Deborës group called upon Tirona Fanatics members to reduce the tensions between the two sets of fans.

The game against Partizani Tirana was seen by attended by 5500 and there were no altercations between rival fans or any offensive chanting but the Albanian Football Association deemed the choreography of the Ujqërit e Dëborës to be worthy of a one match ban on supporters.