The 2016 Indy Eleven season was the club's third season of existence. The club continued to play in North American Soccer League, the second tier of the American soccer pyramid.
<small>Note: Flags indicate national team as has been defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.</small>
In:
Out:
In:
Out:
|- |colspan="14"|Players away on loan:
|- |colspan="14"|Players who left Indy Eleven during the season: