AC Omonia was founded in June 1948. The establishment of the Club (along with that of a few others), was evoked from the political turbulence of that period and the conflict between left-wings and right-wings. In May 1948, APOEL FC sent a letter based on political content to SEGAS (Greek Gymnastic-Athletic Clubs Association), violating the club's statute to not be involved in politics. After that letter, several footballers of the club criticized the their club but that followed the expulsion of those players from the team. Those players with some other people established the new club of Nicosia, with the name Athletic Club Omonia Nicosia.

For that reason several clubs were established and together with Omonia they established the Cyprus Amateur Football Association, since those teams were not accepted as members of the Cyprus Football Association. The new association formed its own competitions, a championship and a cup and lasted until 1953.

The badge of the club is the shamrock. The shamrock represents the strength, the struggle, the insistence of the Omonia founders who were in difficult situation and it is also green which is the colour of the hope. Thus, the colours of the club are the green and the white. The Omonia founders chose the green colour, the "hope's colour", because despite that they were in difficult situation after the political events that took place in Cyprus in 1948, they hoped that better days were coming for the football in Cyprus, and also the new club, Omonia, would have leaded, become poineer and triumph in Cypriot football and also would have been in the conscience of the Cypriot people. A lot people wonder ''What was football in Cyprus be like if the expulsion from APOEL didn't happen'' Until today AC OMONIA and APOEL FC are the two leading teams of the island.