The draw for the third round was held on 12 April 2016, at 16:30 MST (UTC+8), at the Mandarin Oriental Hotel in Kuala Lumpur, Malaysia.

[2][3] The seeding were based on the FIFA World Rankings of April 2016 (shown in parentheses below).

The fixtures of each group were automatically decided based on the respective pot of each team.

Note: Bolded teams qualified for the World Cup.

Italicised teams qualified for the fourth round.