It began on 10 November 1999 with the preliminary round and concluded on 13 May 2000 with the final which was held at GSP Stadium.
Omonia won their 11th Cypriot Cup trophy after beating APOEL 4–2 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.