In the quarter-finals and semi-finals, each tie was played over two legs on a home-and-away basis.
The away goals rule (for two-legged ties), extra time (away goals do not apply in extra time) and penalty shootout would be used to decide the winner if necessary.
[1] The matchups for the round of 16 were decided based on the results from the group stage.
[2] After the completion of the round of 16, the draw for the quarter-finals, semi-finals, and final was held at the AFC house in Kuala Lumpur, Malaysia on 14 June 2012, 15:00 UTC+08:00.
The final of the 2012 AFC Cup was hosted by one of the finalists, decided by a draw.