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.
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.
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.
The schedule of each round was as follows.
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. 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 , at the AFC House in Kuala Lumpur, Malaysia. 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. <section begin=Bracket /> <section end=Bracket />
The first legs were played on 14 and 15 May 2013, and the second legs were played on 21 and 22 May 2013. <section begin=Round of 16 />
|- |+West Zone
|+East Zone
<section end=Round of 16 />
FC Seoul won 3âÂÂ1 on aggregate.
Buriram United won 2âÂÂ1 on aggregate.
Al-Ahli won 3âÂÂ1 on aggregate.
Al-Shabab won 5âÂÂ1 on aggregate.
Kashiwa Reysol won 5âÂÂ2 on aggregate.
Guangzhou Evergrande won 5âÂÂ1 on aggregate.
Lekhwiya won 3âÂÂ2 on aggregate.
Esteghlal won 4âÂÂ2 on aggregate.
The first legs were played on 21 August 2013, and the second legs were played on 18 September 2013. <section begin=Quarter-finals />
<section end=Quarter-finals />
FC Seoul won 2âÂÂ1 on aggregate.
Esteghlal won 3âÂÂ1 on aggregate.
Guangzhou Evergrande won 6âÂÂ1 on aggregate.
3âÂÂ3 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. <section begin=Semi-finals />
<section end=Semi-finals />
Guangzhou Evergrande won 8âÂÂ1 on aggregate.
FC Seoul won 4âÂÂ2 on aggregate.
The first leg was played on 26 October 2013, and the second leg was played on 9 November 2013.
<section begin=Final />
3âÂÂ3 on aggregate. Guangzhou Evergrande won on away goals.<section end=Final />