It began on 14 November 1998 with the preliminary round and concluded on 8 May 1999 with the final that was held at Tsirion Stadium.
APOEL won their 17th Cypriot Cup trophy after beating Anorthosis 2–0 in the final.
If extra time was drawn, there was a replay at the ground of the team who were away for the first game.
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.