[1] The only change to the make-up of the league was the Challenge One winner Munakata Sanix Blues replacing NTT DoCoMo Red Hurricanes.

[3] Unlike previous seasons, there were no title-play-offs, and the team on top of the league after the round-robin stages was crowned the champion.

• Teams 1 to 3 (Green background) advance to the 54th All Japan Rugby Football Championship.

• Team 16 (Red background) will be automatically relegated to the 2017 Top Challenge League.

Coca-Cola Red Sparks, Kintetsu Liners and Toyota Industries Shuttles qualified from the Top League relegation play-off zone, while Hino Red Dolphins, Kyuden Voltex and Mitsubishi Sagamihara DynaBoars qualified from Challenge 1.