The knock-out stage of the 2013 AFC Cup was played from 14 May to 2 November 2013. A total of 16 teams competed in the knock-out stage.[1]
The winners and runners-up of each of the eight groups in the group stage qualified for the knock-out stage. Both West Asia Zone and East Asia Zone had eight teams qualified.
| Group | width=190 | Winners | width=190 | Runners-up |
|---|---|---|---|---|
| West Asia Zone (Groups A–D) | ||||
| A | Al-Kuwait |  Al-Riffa | ||
| B |  Erbil | Fanja | ||
| C |  Al-Faisaly | Dohuk | ||
| D | Al-Qadsia |  Al-Shorta | ||
| East Asia Zone (Groups E–H) | ||||
| E |  Semen Padang |  Kitchee | ||
| F |  New Radiant | Yangon United | ||
| G | Kelantan | SHB Đà Nẵng | ||
| H |  East Bengal | Selangor | ||
In the knock-out stage, the 16 teams played a single-elimination tournament. In the quarter-finals and semi-finals, each tie was played on a home-and-away two-legged basis, while in the round of 16 and final, each tie was played as a single match. The away goals rule (for two-legged ties), extra time (away goals do not apply in extra time) and penalty shoot-out were used to decide the winner if necessary.[1]
The schedule of each round was as follows.[2]
| Round | First leg | Second leg | |
|---|---|---|---|
| Round of 16 | 14–15 May 2013 | ||
| Quarter-finals | 17 September 2013 | 24 September 2013 | |
| Semi-finals | 1 October 2013 | 22 October 2013 | |
| Final | 2 November 2013 | ||
In the round of 16, the winners of one group played the runners-up of another group in the same zone, with the group winners hosting the match.[1] The matchups were determined as follows:
The draw for the quarter-finals, semi-finals, and final (to decide the host team) was held on 20 June 2013, 15:00 UTC+8, at the AFC House in Kuala Lumpur, Malaysia.[3] In this draw, teams from different zones could play each other, and the "country protection" rule was applied: if there are two teams from the same association, they may not play each other in the quarter-finals.
The matches were played on 14 and 15 May 2013.
|-!colspan=3|West Asia Zone|-!colspan=3|East Asia Zone
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The first legs were played on 17 September 2013, and the second legs were played on 24 September 2013.
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East Bengal won 2–1 on aggregate.----2–2 on aggregate. Al-Qadsia won on away goals.----Al-Faisaly won 4–2 on aggregate.----Al-Kuwait won 12–2 on aggregate.
The first legs were played on 1 and 2 October 2013, and the second legs were played on 22 October 2013.
----
Al-Kuwait won 7–2 on aggregate.----Al-Qadsia won 3–1 on aggregate.
See main article: article and 2013 AFC Cup Final.
The final was played on 2 November 2013.