It began on 23 April 1939 with the preliminary round and concluded on 16 July 1939 with the final which was held at GSP Stadium.
AEL won their 1st Cypriot Cup trophy after beating APOEL 3–1 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 a match was drawn, extra time was following.
If extra time was drawn, there was a replay match.