The 2016 NCAA Division III Baseball Tournament was played at the end of the 2016 NCAA Division III baseball season to determine the 41st national champion of college baseball at the NCAA Division III level. The tournament concluded with eight teams competing at Neuroscience Group Field at Fox Cities Stadium in Grand Chute, Wisconsin for the championship. Eight regional tournaments were held to determine the participants in the World Series. Regional tournaments were contested in double-elimination format, with four regions consisting of six teams, and four consisting of eight, for a total of 56 teams participating in the tournament. The tournament champion was Trinity (TX), who defeated Keystone in the championship series in two games.