The 2016 season was the second season of competitive association football played by Bali United Football Club, a professional football club based in Gianyar, Bali, Indonesia. This season, they competed in the Indonesia Soccer Championship A, a football tournament that replaced the temporarily suspended Indonesia Super League.
This season was the first time Bali United ended a full-competition season after 2015 Indonesia Super League was disbanded, having finished in 12th.
|- class="sortbottom" ! colspan="14"| Players transferred out during the season |-
|- class="sortbottom" ! colspan="14"| Players transferred out during the season |-