A total of 6 clubs entered the competition.
It began on 3 February 1946 with the quarterfinals and concluded on 14 April 1946 with the final which was held at GSP Stadium.
EPA won their 2nd Cypriot Cup trophy after beating APOEL 2–1 in the final.
In all rounds each tie was played as a single leg and was held at the home ground of one of the two teams, according to the draw results.
If extra time was drawn, there was a replay match.