| Round of 16 | Quarter-finals | Semi-finals | Final | ||||||||||||||||
|   | 3 | ||||||||||||||||||
|   | 1 | ||||||||||||||||||
|   | 1 | 1 | 2 | ||||||||||||||||
|   | 1 | 0 | 1 | ||||||||||||||||
|   | 1 | ||||||||||||||||||
|   | 3 | ||||||||||||||||||
|   | 2 | 1 | 3 | ||||||||||||||||
|   | 1 | 0 | 1 | ||||||||||||||||
|   | 0 (1) | ||||||||||||||||||
|   | 0 (3) | ||||||||||||||||||
|   | 5 | 0 | 5 | ||||||||||||||||
|   | 4 | 1 | 5 | ||||||||||||||||
|   | 4 | ||||||||||||||||||
|   | 0 | ||||||||||||||||||
|   | 2 | ||||||||||||||||||
|   | 1 | ||||||||||||||||||
|   | 4 | ||||||||||||||||||
|   | 0 | ||||||||||||||||||
|   | 2 | 0 | 2 | ||||||||||||||||
|   | 2 | 2 | 4 | ||||||||||||||||
|   | 8 | ||||||||||||||||||
|   | 2 | ||||||||||||||||||
|   | 2 | 0 | 2 | ||||||||||||||||
|   | 1 | 3 | 4 | ||||||||||||||||
|   | 1 | ||||||||||||||||||
|   | 2 | ||||||||||||||||||
|   | 0 | 0 | 0 (5) | ||||||||||||||||
|   | 0 | 0 | 0 (4) | ||||||||||||||||
|   | 2 | ||||||||||||||||||
|   | 1 | ||||||||||||||||||
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.
|  Al-Zawraa   | 1–3 |   | 
|---|---|---|
| Adnan Attiya  | Report |  Ahmad Salah  Luay Salah Ahmad Abd Ali  | 
|  Al-Kuwait   | 3–1 |   | 
|---|---|---|
|  Al Hussain  | Report |  Roberto Mendes Silva  | 
|  Al-Majd   | 0–0 (a.e.t.) |   | 
|---|---|---|
| Report | ||
| Penalties | ||
|  Al Zeno  Asaad Diab Kaddour  | 1–3 | |
|  Bình Dương   | 8–2 |   | 
|---|---|---|
|  Helio  Nguyễn Vũ Phong Kesley Nguyễn Đức Thiện Nguyễn Anh Đức  | Report |  Shahrul  Azrul  | 
|  Chonburi   | 4–0 |   | 
|---|---|---|
|  Kone  Inthasen  | Report | 
|  South China   | 4–0 |   | 
|---|---|---|
|  Kwok Kin Pong  Li Haiqiang Cacá  | Report | 
The draw for the quarter-finals and the remaining knockout rounds took place at Kuala Lumpur, Malaysia on June 29, 2009.
|  Chonburi   | 2–2 |   | 
|---|---|---|
|  On-Mo  Sunthornpit  | Report |  Huỳnh Quang Thanh  Nguyễn Vũ Phong  | 
|  Neftchi Farg'ona   | 5–4 |   | 
|---|---|---|
|  Saidov  Berdiyev  | Report |  Gerard  Ramón Kwok Kin Pong Carrijo  | 
|  Al-Karamah   | 0–0 |   | 
|---|---|---|
| Report | 
|  Bình Dương   | 2–0 |   | 
|---|---|---|
|  Philani  Molina  | Report | 
Bình Dương won 4–2 on aggregate.
|  South China   | 1–0 |   | 
|---|---|---|
|  Carrijo  | Report | 
5–5 on aggregate. South China won on away goals.
|  Arbil   | 0–1 |   | 
|---|---|---|
| Report |  Rogerio  | 
Al-Kuwait won 2–1 on aggregate.
|  Al-Arabi   | 0–0 (a.e.t.) |   | 
|---|---|---|
| Report | ||
| Penalties | ||
|  Jarragh  Maqseed Moussawi Khalaf Ashkanani Rashidi  | 4–5 | |
0–0 on aggregate. Al-Karamah won 5–4 on penalties.
|  Bình Dương   | 2–1 |   | 
|---|---|---|
|  Trần Chí Công  Philani  | Report |  Omaier  | 
|  Al-Kuwait   | 2–1 |   | 
|---|---|---|
|  Al Marzooqi  Sulaiman  | Report |  Gerard  | 
|  South China   | 0–1 |   | 
|---|---|---|
| Report |  Sulaiman  | 
Al-Kuwait won 3–1 on aggregate.
|  Al-Karamah   | 3–0 |   | 
|---|---|---|
|  Al Hamawi  | Report | 
Al-Karamah won 4–2 on aggregate.
The 2009 AFC Cup Final was played on November 3 at the home ground of Al Kuwait. [1]