* – Provisional Division III member ** – Dean was accepted as a Division III football program for the 2016 season and finished with a 6–4 overall record, but only two games were against varsity level teams.
Twenty-five conferences met the requirements for an automatic ("Pool A") bid to the playoffs. Besides the NESCAC, which does not participate in the playoffs, two conferences had no Pool A bid. The American Southwest, which had fallen below the required seven members in 2013 and lost its Pool A bid after the two-year grace period, was in the first year of the two-year waiting period, having now attained seven members; the SCAC had only four members.
Schools not in Pool A conferences were eligible for Pool B. The number of Pool B bids was determined by calculating the ratio of Pool A conferences to schools in those conferences and applying that ratio to the number of Pool B schools. The 25 Pool A conferences contained 222 schools, an average of 8.9 teams per conference. Twelve schools were in Pool B, enough for one bid.
The remaining six playoff spots were at-large ("Pool C") teams.
First round November 19, 2016
Second round November 26, 2016
Quarterfinals December 3, 2016
Semifinals December 10, 2016
Championship December 16, 2016 Salem Football Stadium Salem, Virginia