APOP Kinyras won their 1st Cypriot Cup trophy after beating AEL 2–0 in the final.
Teams from the two lower divisions (Third and Fourth) competed in a separate cup competition.
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.
The four first division teams which were qualified for 2007–08 Cypriot Cup's semifinals (APOEL, Anorthosis, Apollon, Omonia) did not participated in this round.
The draw for the semifinals took place at the Hilton Park hotel in Nicosia on March 20, 2009.