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.
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).
The schedule of each round was as follows.
The bracket of the knockout stage was determined as follows:
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.