The 2016 AFC Champions League knockout stage was played from 17 May to 26 November 2016. A total of 16 teams competed in the knockout stage to decide the champions of the 2016 AFC Champions League.
The winners and runners-up of each of the eight groups in the group stage qualified for the knockout stage. Both West Zone and East Zone had eight qualified teams. <section begin=Qualified teams /> <section end=Qualified teams />
<section begin=Format /> In the knockout stage, the 16 teams played a single-elimination tournament, with the teams split between the two zones until the final. 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 (Regulations Article 12.3).<section end=Format />
The schedule of each round was as follows.
The bracket of the knockout stage was determined as follows:
<section begin=Bracket /> <section end=Bracket />
<section begin=Round of 16 /> In the round of 16, the winners of one group played the runners-up of another group from the same zone, with the group winners hosting the second leg.
|- |+West Zone
|+East Zone
<section end=Round of 16 />
Lokomotiv Tashkent won 2âÂÂ1 on aggregate.
Al-Nasr won 5âÂÂ4 on aggregate.
Al-Ain won 3âÂÂ1 on aggregate.
El Jaish won 6âÂÂ4 on aggregate.
Jeonbuk Hyundai Motors won 3âÂÂ2 on aggregate.
2âÂÂ2 on aggregate. Shanghai SIPG won on away goals.
3âÂÂ3 on aggregate. FC Seoul won 7âÂÂ6 on penalties.
3âÂÂ3 on aggregate. Shandong Luneng won on away goals.
<section begin=Quarter-finals /> In the quarter-finals, the four teams from the West Zone were drawn into two ties, and the four teams from the East Zone were drawn into the other two ties, with the order of legs also decided by the draw.
The draw for the quarter-finals was held on 9 June 2016, 16:00 MYT (), at the Petaling Jaya Hilton Hotel in Kuala Lumpur, Malaysia. There was no seeding or country protection, so teams from the same association could be drawn into the same tie.
|- |+West Region
|+East Region
<section end=Quarter-finals />
Al-Ain won 1âÂÂ0 on aggregate.
The El Jaish v Al-Nasr first leg, originally won 3âÂÂ0 by Al-Nasr, was forfeited and awarded 3âÂÂ0 to El Jaish by the AFC Disciplinary Committee on 12 September 2016, as Al-Nasr fielded the player Wanderley, who was found to be registered using a fake Indonesian passport.
El Jaish won 4âÂÂ0 on aggregate.
Jeonbuk Hyundai Motors won 5âÂÂ0 on aggregate.
FC Seoul won 4âÂÂ2 on aggregate.
<section begin=Semi-finals /> In the semi-finals, the two quarter-final winners from the West Zone play each other, and the two quarter-final winners from the East Zone play each other, with the order of legs determined by the quarter-final draw.
|- |+West Region
|+East Region
<section end=Semi-finals />
Al-Ain won 5âÂÂ3 on aggregate.
Jeonbuk Hyundai Motors won 5âÂÂ3 on aggregate.
<section begin=Final /> In the final, the two semi-final winners play each other, with the order of legs reversed from the previous season's final, with the team from the East Zone hosting the first leg, and the team from the West Zone hosting the second leg.<noinclude>
</noinclude>
Jeonbuk Hyundai Motors won 3âÂÂ2 on aggregate.<section end=Final />