With the Asian Football Confederation reviewed the format of the AFC Champions League and made significant changes to way the competition is run, the teams that qualified for the AFC Cup is also from different countries compared to the previous editions.

Each club plays double round-robin (home and away) against fellow three group members, a total of 6 matches each.

The clubs are ranked according to points and tie breakers are in following order: Winners and runners-up of each group will qualify for the next round.

The draw for the quarter-finals and the remaining knockout rounds took place at Kuala Lumpur, Malaysia on 29 June 2009 starting 7:30 pm.

The 2009 AFC Cup Final was played on 3 November at the home ground of Al Kuwait.