The participants of the 2016 NCAA Division I Football Championship Game were the finalists of the 2015 FCS Playoffs, which began with a 24-team bracket. No. 1 seed Jacksonville State and No. 3 seed North Dakota State qualified for the final by winning their semifinal games.
The Gamecocks, led by second-year head coach John Grass, finished the regular season 10–1, 8–0 in OVC play, to earn a conference championship and the No. 1 seed in the FCS Playoffs. Jacksonville State defeated unseeded Chattanooga, No. 8 seed Charleston Southern, and unseeded Sam Houston State to reach their first ever final.
The Bison, led by second-year head coach Chris Klieman, finished the regular season 8–2, 7–1 in MVFC play, to earn a conference co-championship (shared with Illinois State) and the No. 3 seed in the FCS Playoffs. North Dakota State defeated unseeded Montana, unseeded Northern Iowa, and No. 7 seed Richmond to reach the final. The Bison entered the Championship game with a 4–0 record in previous FCS Championships, having won the last four straight.