It began on 16 November 1988 with the first preliminary round and concluded on 10 June 1989 with the final which was held at Tsirion Stadium.
AEL Limassol won their 6th Cypriot Cup trophy after beating Aris 3–2 in the final.
In the preliminary 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 both teams had scored the same number of home and away goals, then extra time was following after the end of the second leg match.
If there weren't scored any goals during extra time, the qualifying team was determined by penalty shoot-out.