The knock-out stage of the 2013 AFC Champions League was played from 14 May to 9 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 Zone and East Zone had eight teams qualified.
| Group | width=190 | Winners | width=190 | Runners-up |
|---|---|---|---|---|
| West Zone (Groups A–D) | ||||
| A | Al-Shabab |  El Jaish | ||
| B | Lekhwiya | Al-Shabab Al-Arabi | ||
| C | Al-Ahli | Al-Gharafa | ||
| D |  Esteghlal | Al-Hilal | ||
| East Zone (Groups E–H) | ||||
| E |  FC Seoul |  Buriram United | ||
| F |  Guangzhou Evergrande | Jeonbuk Hyundai Motors | ||
| G |  Bunyodkor | Beijing Guoan | ||
| H |  Kashiwa Reysol |  Central Coast Mariners | ||
In the knock-out stage, the 16 teams played a single-elimination tournament. Each tie was played on a home-and-away two-legged basis. The away goals rule, 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 | 21–22 May 2013 | |
| Quarter-finals | 21 August 2013 | 18 September 2013 | |
| Semi-finals | 25 September 2013 | 2 October 2013 | |
| Final | 25 or 26 October 2013 | 8 or 9 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 second leg.[1] The matchups were determined as follows:
The draw for the quarter-finals, semi-finals, and final (to decide the order of two legs) was held on 20 June 2013, 16:00 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 exactly two teams from the same association, they may not play each other in the quarter-finals; however, if there are more than two teams from the same association, they may play each other in the quarter-finals.
The first legs were played on 14 and 15 May 2013, and the second legs were played on 21 and 22 May 2013.|-|+West Zone|}|+East Zone|}
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FC Seoul won 3–1 on aggregate.----Buriram United won 2–1 on aggregate.----Al-Ahli won 3–1 on aggregate.----Al-Shabab won 5–1 on aggregate.----Kashiwa Reysol won 5–2 on aggregate.----Guangzhou Evergrande won 5–1 on aggregate.----Lekhwiya won 3–2 on aggregate.----Esteghlal won 4–2 on aggregate.
The first legs were played on 21 August 2013, and the second legs were played on 18 September 2013.|}
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FC Seoul won 2–1 on aggregate.----Esteghlal won 3–1 on aggregate.----Guangzhou Evergrande won 6–1 on aggregate.----3–3 on aggregate. Kashiwa Reysol won on away goals.
The first legs were played on 25 September 2013, and the second legs were played on 2 October 2013.|}
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Guangzhou Evergrande won 8–1 on aggregate.----FC Seoul won 4–2 on aggregate.
See main article: 2013 AFC Champions League Final.
The first leg was played on 26 October 2013, and the second leg was played on 9 November 2013.
|}3–3 on aggregate. Guangzhou Evergrande won on away goals.