The Suntory Sungoliath team defeated Sanyo Wild Knights by 47–28 in the final of the Microsoft Cup to claim their second Top League championship.

• The top 4 teams also qualified for entry into the All-Japan Rugby Football Championship.

• Teams 5 to 8 qualified for the wildcard play-offs for entry into the All-Japan Rugby Football Championship.

The top 4 teams of 2011–12 were Suntory Sungoliath, Toshiba Brave Lupus, Sanyo Wild Knights, and NEC Green Rockets.

Canon Eagles and Kyuden Voltex won promotion to the 2012–13 Top League via the 2011–12 Top League Challenge Series, while Kubota Spears and Toyota Industries Shuttles progressed to the promotion play-offs.