The 2016 NAIA football national championship was a four-round, sixteen team tournament played between November 19 and December 17 of 2016.

The tournament concluded on December 17 with a single game, played as the 61st Annual NAIA Football National Championship Presented by Waste Pro.

Waste Pro became the newest title game sponsor in an announcement made October 31, 2015.

[1] The game featured two teams that had never before won a national championship, the undefeated #2 Baker Wildcats facing the once-beaten #4 Saint Francis Cougars.

The field was filled with at-large selections that were awarded to the highest ranked teams that were not conference champions.