It began on 10 September 2005 with the first round and concluded on 13 May 2006 with the final which was held at GSZ Stadium.
APOEL won their 18th Cypriot Cup trophy after beating AEK 3–2 (aet) in the final.
In the first and in the second round 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.
FC Episkopi and Kissos Kissonerga which finished first and second in the 2005 STOK promotion play-offs, participated in the Cypriot Cup.
The first four teams of the 2004–05 Cypriot First Division (Anorthosis, APOEL, Omonia, Olympiakos) were set heads of each group and the 5th–8th placed teams (Digenis, Nea Salamina, Apollon and Enosis Neon Paralimni) were drawn one per group.
[1] The second leg match between Anorthosis and AEK was abandoned in the 55th minute due to floodlight failure and was replayed on 19 April.