[1] A total of 16 teams competed in the knockout stage to decide the champions of the 2016 AFC Cup.
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).
[2] 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).
[4] The draw for the quarter-finals was held on 9 June 2016, 15:00 MYT (UTC+8), at the Petaling Jaya Hilton Hotel in Kuala Lumpur, Malaysia.
[5] There was no seeding or country protection, so teams from the same association could be drawn into the same tie.