The knock-out stage of the 2013 AFC Cup was played from 14 May to 2 November 2013.
In the knock-out stage, the 16 teams played a single-elimination tournament.
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 do not apply in extra time) and penalty shoot-out were used to decide the winner if necessary.
[1] The matchups were determined as follows: The draw for the quarter-finals, semi-finals, and final (to decide the host team) was held on 20 June 2013, 15:00 UTC+8, at the AFC House in Kuala Lumpur, Malaysia.