| Round of 16 | Quarter-finals | Semi-finals | Final | ||||||||||||||||
 Al-Kuwait
| 3 | ||||||||||||||||||
 Dempo
| 1 | ||||||||||||||||||
| Al-Kuwait
| 1 | 1 | 2 | ||||||||||||||||
 Arbil
| 1 | 0 | 1 | ||||||||||||||||
| Al-Zawraa
| 1 | ||||||||||||||||||
| Arbil
| 3 | ||||||||||||||||||
| Al-Kuwait
| 2 | 1 | 3 | ||||||||||||||||
 South China
| 1 | 0 | 1 | ||||||||||||||||
 Al-Majd
| 0 (1) | ||||||||||||||||||
 Neftchi Farg'ona (p)
| 0 (3) | ||||||||||||||||||
| Neftchi Farg'ona
| 5 | 0 | 5 | ||||||||||||||||
| South China (a)
| 4 | 1 | 5 | ||||||||||||||||
| South China
| 4 | ||||||||||||||||||
 Home United
| 0 | ||||||||||||||||||
| Al-Kuwait
| 2 | ||||||||||||||||||
| Al-Karamah
| 1 | ||||||||||||||||||
 Chonburi
| 4 | ||||||||||||||||||
 PSMS Medan
| 0 | ||||||||||||||||||
| Chonburi
| 2 | 0 | 2 | ||||||||||||||||
 Binh Duong
| 2 | 2 | 4 | ||||||||||||||||
| Binh Duong
| 8 | ||||||||||||||||||
 Kedah
| 2 | ||||||||||||||||||
| Binh Duong
| 2 | 0 | 2 | ||||||||||||||||
| Al-Karamah
| 1 | 3 | 4 | ||||||||||||||||
 Busaiteen
| 1 | ||||||||||||||||||
| Al-Karamah (a.e.t.)
| 2 | ||||||||||||||||||
| Al-Karamah (p)
| 0 | 0 | 0 (5) | ||||||||||||||||
| Al-Arabi
| 0 | 0 | 0 (4) | ||||||||||||||||
| Al-Arabi (a.e.t.)
| 2 | ||||||||||||||||||
 Safa
| 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 | Arbil |
|---|---|---|
Adnan Attiya  76' |
Report | Ahmad Salah 44' Luay Salah 67'Ahmad Abd Ali 70' |
Attendance: 200
Referee: Abdulrahman Abdou (Qatar)
| Busaiteen | 1–2 (a.e.t.) | Al-Karamah |
|---|---|---|
| Akaruye 57' (pen.) |
Report | Al Hamawi 43' Abbas 116' |
Attendance: 300
Referee: Mohammed Al Saeedi (UAE)
| Al-Kuwait | 3–1 | Dempo |
|---|---|---|
| Al Hussain 21' (pen.), 58', 90+5' (pen.) |
Report | Roberto Mendes Silva 73' |
Referee: Abdullah Al Hilali (Oman)
| Al-Majd | 0–0 (a.e.t.) | Neftchi Farg'ona |
|---|---|---|
| Report | ||
| Penalties | ||
Al Zeno  Asaad Diab  Kaddour |
1–3 | Boqiyev Tukhtahujaev Kholikov Nizametdinov |
Attendance: 6,000
Referee: Tan Hai (China)
| Al-Arabi | 2–1 (a.e.t.) | Safa |
|---|---|---|
| Ezukam 29' Al Khatib 112' |
Report | Al Saadi 59' |
Attendance: 3,400
Referee: Mohsen Torky (Iran)
| Bình Dương | 8–2 | Kedah |
|---|---|---|
| Helio 17' Nguyễn Vũ Phong 19'Kesley 39', 70', 81', 90+2'Nguyễn Đức Thiện 41'Nguyễn Anh Đức 78' |
Report | Shahrul 69' Azrul 89' (pen.) |
Attendance: 18,000
Referee: Minoru Tojo (Japan)
| Chonburi | 4–0 | PSMS Medan |
|---|---|---|
| Kone 19', 67', 90+3' Inthasen 87' |
Report |
Attendance: 6,000
Referee: Almarzouqi Hassan (UAE)
| South China | 4–0 | Home United |
|---|---|---|
| Kwok Kin Pong 19' Li Haiqiang 21', 64' (pen.)Cacá 51' |
Report |
Attendance: 8,972
Referee: Abdullah Balideh (Qatar)
The draw for the quarter-finals and the remaining knockout rounds took place at Kuala Lumpur, Malaysia on June 29, 2009.
| Chonburi | 2–2 | Bình Dương |
|---|---|---|
| On-Mo 20' Sunthornpit 70' |
Report | Huỳnh Quang Thanh 14' Nguyễn Vũ Phong 24' |
Attendance: 4,500
Referee: Tayeb Hasan Shamsuzzaman (Bangladesh)
| Neftchi Farg'ona | 5–4 | South China |
|---|---|---|
| Saidov 5' Berdiyev 34', 44', 79', 90+4' |
Report | Gerard 33' Ramón 35'Kwok Kin Pong 41'Carrijo 84' |
Attendance: 13,500
Referee: Mohamed Masoud (Oman)
| Al-Kuwait | 1–1 | Arbil |
|---|---|---|
| Al Azemi 7' |
Report | Mahdi 68' |
Attendance: 2,800
Referee: Abdul Malik (Singapore)
| Al-Karamah | 0–0 | Al-Arabi |
|---|---|---|
| Report |
Attendance: 30,000
Referee: Valentin Kovalenko (Uzbekistan)
| Bình Dương | 2–0 | Chonburi |
|---|---|---|
| Philani 57' Molina 86' |
Report |
Attendance: 24,000
Referee: Peter Green (Australia)
Bình Dương won 4–2 on aggregate.
| South China | 1–0 | Neftchi Farg'ona |
|---|---|---|
| Carrijo 2' |
Report |
Attendance: 20,112
Referee: Minoru Tojo (Japan)
5–5 on aggregate. South China won on away goals.
| Arbil | 0–1 | Al-Kuwait |
|---|---|---|
| Report | Rogerio 74' |
Referee: Mohsen Torky (Iran)
Al-Kuwait won 2–1 on aggregate.
| Al-Arabi | 0–0 (a.e.t.) | Al-Karamah |
|---|---|---|
| Report | ||
| Penalties | ||
| Jarragh Maqseed Moussawi Khalaf Ashkanani Rashidi |
4–5 | Abbas Jenyat Ibrahim Awde Hamawi Mando |
Attendance: 5,000
Referee: Hassan Al Marzouqi (UAE)
0–0 on aggregate. Al-Karamah won 5–4 on penalties.
| Bình Dương | 2–1 | Al-Karamah |
|---|---|---|
| Trần Chí Công 19' Philani 42' |
Report | Omaier 68' |
Attendance: 20,000
Referee: Hiroyoshi Takayama (Japan)
| Al-Kuwait | 2–1 | South China |
|---|---|---|
| Al Marzooqi 48' Sulaiman 79' |
Report | Gerard 90+2' |
Attendance: 2,000
Referee: Abdulrahman Abdou (Qatar)
| South China | 0–1 | Al-Kuwait |
|---|---|---|
| Report | Sulaiman 82' |
Attendance: 37,459
Referee: Mohammad Omar Al Saeedi (UAE)
Al-Kuwait won 3–1 on aggregate.
| Al-Karamah | 3–0 | Bình Dương |
|---|---|---|
| Al Hamawi 18', 36', 59' |
Report |
Attendance: 23,000
Referee: Tan Hai (China)
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]
| Al-Kuwait | 2–1 | Al-Karamah |
|---|---|---|
| Hakem 16' Sulaiman 90+4' |
Report | Al Shbli 82' |
Attendance: 17,400
Referee: Masoud Moradi (Iran)