The competition began on 25 October 2008 with the first round and ended on 9 May 2009 with the final.

Linfield were the defending champions, winning their third consecutive Irish Cup the previous season after a 2–1 win over Coleraine in the 2008 final.

This season they reached the semi-finals, but were defeated by Cliftonville.

Crusaders went on to lift the trophy, beating Cliftonville 1–0 in the final.

In doing so, they earned a place in the second qualifying round of the 2009–10 UEFA Europa League.