In the knockout stage, the 11 teams played a single-elimination tournament, with the teams split into the five zones until the Inter-zone play-off semi-finals. Each tie was played on a home-and-away two-legged basis, except the final which 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 11.3).
The schedule of each round was as follows (W: West Asia Zone; A: ASEAN Zone). Matches in the West Asia Zone were played on Mondays and Tuesdays, while matches in the ASEAN Zone and the Inter-zone play-offs were played on Tuesdays and Wednesdays.
In the Zonal semi-finals, the four qualified teams from the West Asia Zone (Groups A–C) played in two ties, and the four qualified teams from the ASEAN Zone (Groups F–H) played in two ties, with the matchups and order of legs determined by the group stage draw and identity of the best runner-up.
The draw for the Zonal finals was held on 6 June 2017. In the Zonal finals, the two winners of West Asia Zonal semi-finals played each other, and the two winners of ASEAN Zonal semi-finals played each other, with the order of legs decided by draw. The winner of the West Asia Zonal final advanced to the final, while the winner of the ASEAN Zonal final advanced to the Inter-zone play-off semi-finals.
The draw for the Inter-zone play-off semi-finals was held on 6 June 2017. In the Inter-zone play-off semi-finals, the four zonal winners other than the West Asia Zone played in two ties, i.e., the winner of the Central Asia Zone (Group D), the winner of the South Asia Zone (Group E), the winner of the East Asia Zone (Group I), and the winner of the ASEAN Zonal final (whose identity was not known at the time of the draw), with the matchups and order of legs decided by draw, without any seeding.
In the Inter-zone play-off final, the two winners of the Inter-zone play-off semi-finals played each other, with the order of legs determined by the Inter-zone play-off semi-final draw. The winner of the Inter-zone play-off final advanced to the final.
The draw for the final was held on 6 June 2017. In the final, the winner of the West Asia Zonal final and the winner of the Inter-zone play-off final played each other, with the host team decided by draw.
^ abcThe West Asia Zonal semi-final first leg between Al-Quwa Al-Jawiya and Al-Zawraa was agreed by the AFC to be staged in Iraq following FIFA's approval in May 2017 to allow international matches to be played there, and to allow logistical preparation, was moved from 15 May to 22 May. The second leg was also expected to be played in Iraq, but the home side Al-Zawraa requested that it be played in Qatar. The West Asia Zonal final second leg between Al-Quwa Al-Jawiya and Al-Wahda was also played in Qatar.
^ abTeams from Syria are not allowed to host their home matches in their country due to security concerns.