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Foundation and first years

The club was established in 2012, after the merger of AO Arta, Aetos Diasello and Omonoia Petra, and is currently competing in the 2nd tier of Greek football, the Super League Greece 2. In the 2014–15 Football League 2, despite leading the table for a big part of the season, and having the best attacking and defensive record of the group, scoring 60 and conceding just 14, Karaiskakis lost to AO Trikala on the last matchday with a score of 1–2, a result that led to the club missing out on promotion to Beta Ethniki.

2015–16 season

The 2015–16 season for Karaiskakis started with an away victory of 1–2 at Farkadona. The first home match was against nearby Ethnikos Filippiada, and ended in a goalless draw. Karaiskakis played their first match at their official home on 25/10/2015 against Niki Volos. The game ended 2–1 in favour of Karaiskakis, who came back to win after being 0–1 down at half-time. On November 5, 2015, after disagreements in a meeting session, former coach, Sakis Papavasileiou, terminated his contract with the club. Three days later, the club announced the hiring of the 54 year old coach from Arta, Giannis Taprantzis. Having been in charge for only 3 games, Taprantzis left the club for personal reasons. After a few days, Giorgos Giannos became the club's new manager. The very next day after the hiring of Giannos, Karaiskakis defeated Pyrasos 4–0 at home. The first defeat of the season came against Aiginiakos on the 13th matchday, with a score of 3–1. On the final day of the first round, Karaiskakis defeated Rigas Feraios 2–1, coming back after conceding in the 42nd minute. That same year, Karaiskakis won for the first time in his history the FCA Arta's Cup.

Recent years

In September 2016, a joint announcement was made with the administration of the Renaissance Arta on the cooperation and common course of the two groups. The co-operation eventually did not materialize. At the end of the 2016–17 season, the team finished second in the third consecutive year. After the end of the championship, the team managed to win the Gamma Ethniki Cup 2016–17. As Cupid, they claimed with Irodotos the Super Cup of Amateur Football of Greece where they were defeated by 1–0.

Promotion to the Football League

In the summer of 2017, HFF initially decided to fill the gap of a team in the 2nd national with the third rounds of the 2016–17 Gamma Ethniki, provided that they will deposit a €300,000 guarantee. The only groups that did it were Karaiskakis and Doxa Drama. The barrage was set to be in Katerini. Finally, with a new decision, EPO abolished the barrage of climb. Following the appeal of Doxa Dramas against the decision of the HFF, the HFF Arbitration Court decided to become the barrage. After the withdrawal of Iraklis from the Football League, the match was canceled and the two teams were promoted to the Football League.