The 2016 AFC Cup knockout stage was played from 24 May to 5 November 2016. A total of 16 teams competed in the knockout stage to decide the champions of the 2016 AFC Cup.
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. 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 would not apply in extra time) and penalty shoot-out were used to decide the winner if necessary (Regulations Article 12.4).
Starting from this season, the knockout stage was split between the two zones until the final, similar to the AFC Champions League (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 match.
|- !colspan=3|West Zone
|- !colspan=3|East Zone
<section end=Round of 16 />
<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, 15:00 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.
|- !colspan=5|West Zone
|- !colspan=5|East Zone
<section end=Quarter-finals />
Al-Quwa Al-Jawiya won 5âÂÂ1 on aggregate.
Al-Ahed won 3âÂÂ0 on aggregate.
Johor Darul Ta'zim won 3âÂÂ2 on aggregate.
Bengaluru won 1âÂÂ0 on aggregate.
<section begin=Semi-finals /> In the semi-finals, the two quarter-final winners from the West Zone played each other, and the two quarter-final winners from the East Zone played each other, with the order of legs determined by the quarter-final draw.
|- !colspan=5|West Zone
|- !colspan=5|East Zone
<section end=Semi-finals />
Al-Quwa Al-Jawiya won 4âÂÂ3 on aggregate.
Bengaluru won 4âÂÂ2 on aggregate.
<section begin=Final /> In the final, the two semi-final winners played each other, with the host team decided by a draw, held after the quarter-final draw.<noinclude>
</noinclude>
<section end="Final" />