In the 2008–09 Cypriot Cup, participated all the teams of the
Cypriot First Division and the
Cypriot Second Division. Teams from the two lower divisions (
Third and
Fourth) competed in a
separate cup competition. The competition consisted of five rounds. All rounds, except the final, were played in a two-legged format, each team playing a home and an away match against their opponent. The team which scored more goals on aggregate, was qualifying to the next round. If the two teams scored the same number of goals on aggregate, then the team which scored more goals away from home was advancing to the next round. 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 during the extra thirty minutes both teams had managed to score, but they had scored the same number of goals, then the team who scored the away goals was advancing to the next round (i.e. the team which was playing away). If there weren't scored any goals during extra time, the qualifying team was determined by
penalty shoot-out. The final was a single match. The cup winner secured a place in the
2009–10 UEFA Europa League. ==Bracket==