The Toshiba Brave Lupus defeated Sanyo Wild Knights by 17–6 in the final of the Microsoft Cup to claim the 2008–09 Top League championship.

• The top 6 teams also qualified for entry into the All-Japan Rugby Football Championship.

The top 4 teams of 2008–09 were Toshiba Brave Lupus, Sanyo Wild Knights, Kobe Steelers and Suntory Sungoliath.

Honda Heat and Ricoh Black Rams won promotion to the 2009–10 Top League via the 2009 Top League Challenge Series, while Mazda Blue Zoomers and Toyota Industries Shuttles progressed to the promotion play-offs.

Two promotion/relegation matches (Irekaesen) were played with the winners qualifying for the Top League in the next season.