A total of 24 teams entered the qualification tournament, which decided four of the eight participating teams in the final tournament held in Thailand.

Of the 47 AFC member associations, a total of 27 teams entered the competition, with North Korea, Japan, China and the host nation Thailand automatically qualified for the final tournament by their position as the top four teams of the 2015 AFC U-16 Women's Championship and thus did not participate in the qualifying competition, except for Thailand which decided to also participate in the qualifying competition.

The draw for the qualifiers was held on 19 May 2016, 15:00 MYT (UTC+8), at the AFC House in Kuala Lumpur, Malaysia.

The teams were seeded according to their performance in the previous season in 2015 AFC U-16 Women's Championship final tournament and qualification.

The following restrictions were also applied:[3] Players born between 1 January 2001 and 31 December 2003 were eligible to compete in the 2017 AFC U-16 Women's Championship.