The Indonesian Football Association was suspended by football's world governing body FIFA because of government interference in the Southeast Asian country's national league on 30 May 2015 but this was lifted on 13 May 2016.

All twelve member associations of the ASEAN Football Federation were set to take part in the tournament featuring three groups of four teams, but with Indonesia's suspension, they were omitted and the AFF reverted to two groups featuring six and five teams.

The following groups were drawn at the AFF Council meeting in Da Nang, Vietnam on 13 March 2016.

Thailand (1) Myanmar (2) Australia (3) Laos (4) Timor-Leste (5) Singapore (6) Cambodia (7) Malaysia (8) Vietnam (9) Brunei (10) Philippines (11) The top two teams of each group advance to the semi-finals.

In the knockout stage, penalty shoot-out is used to decide the winner if necessary (extra time is not used).