[2] The Sanix Blues team was relegated, and Coca-Cola West Red Sparks, Kubota Spears, Toyota Industries were promoted to the Top League for 2013–14.

The teams in Group 2 ranked 5th to 7th went through to the promotion and relegation play-offs against regional challengers to fight to remain in the Top League.

• Teams 5 to 8 (Blue background) qualify for the wildcard play-offs for entry into the All-Japan Rugby Football Championship.

• Teams 5 to 7 (Yellow background) go through to the promotion and relegation play-offs against regional challengers to retain their places in the Top League.

If teams are level at any stage, tiebreakers are applied in the following order: • Difference between points for and against • Total number of points for • Number of matches won • Aggregate number of points scored in matches between tied teams Top 4 sides of the regular season competed in the Microsoft Cup (2014) knock out tournament to fight for the Top League title.

The top 4 teams of 2013–14 were Panasonic Wild Knights, Suntory Sungoliath, Kobelco Steelers, and Toshiba Brave Lupus.

Fukuoka Sanix Blues won promotion to the 2014–15 Top League via the 2013–14 Top League Challenge Series, while Honda Heat, Mitsubishi Sagamihara DynaBoars and Yokogawa Musashino Atlastars progressed to the promotion play-offs.