2009 AFC Cup knockout stage

Round of 16
The draw for the round of 16 of the 2009 AFC Cup was held on 12 January 2009, along with the draw for the group stage.

Quarter-finals
The draw for the quarter-finals and the remaining knockout rounds took place at Kuala Lumpur, Malaysia on June 29, 2009.

Second leg
Bình Dương won 4–2 on aggregate.

''5–5 on aggregate. South China won on away goals.''

Al-Kuwait won 2–1 on aggregate.

''0–0 on aggregate. Al-Karamah won 5–4 on penalties.''

Second leg
Al-Kuwait won 3–1 on aggregate.

Al-Karamah won 4–2 on aggregate.

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