The club was established in 1963 when three local football clubs (Aris, Atromitos and Orestias) merged to form one stronger team representing the town. In 1974, Kastoria played for the first time in the A' Ethniki of the Greek National League. Kastoria have played in the A' Division from 1974–1983 and again in season 1996-1997.
Kastoria FC, throughout its 50 year history, has been handled by several different owners and Presidents. Its golden era was between 1974 and 1983, when the club remained for 9 consecutive years amongst Greece’s top elite clubs, achieving the most important trophy of its history: The Greek Cup (1979/80). During this golden period, two Presidents distinguished themselves, Sotiris Sianos and Giorgos Chalkidis.
Another important presence in Kastoria’s history was Mr. Panagiotis Spyropoulos, one of the world’s largest furs trades, who handled the club’s affairs as owner (and occasionally President), between 1999 and 2009. During Spyropoulos tenure, Kastoria failed to achieve the desired return to Greece’s highest football division, remaining mostly in the 2nd Divisions.
After Mr. Spyropoulos departed the club in 2009, with the club in the 3rd Division, Kastoria not only failed to re-establish itself as a football force, but also faced the deepest crisis of its history, being relegated to the 4th Division and to the local the local Amateur Division in the following years.
After a very hard work from the local members of the Amateur club, Kastoria finally managed to return to Greece’s 3rd Division in the 2013/14 season and, in February 2014, a group of Brazilian sport’s related professional accepted to take the responsibility of running the club, with the ambitious objectives to rebuild the Kastoria Football Brand and to bring the club back to the country’s highest football level (Super League). Mr. Nikolaos Pepelidis, was elected President of the club.