Top League

The top four teams (Suntory Sungoliath, Sanyo Wild Knights, Toshiba Brave Lupus, NEC Green Rockets) in the 2011–12 Top League automatically qualified for the competition, and competed in a playoff competition.

Sanyo Wild Knights and Suntory Sungoliath eventually played in the Final, with Suntory Sungoliath winning 47–28. As Top League finalists they gained automatic entry to the Championship Semi-finals.

The Top League Wildcard Tournament was contested by the fifth to tenth teams in the final table for the last two places for this league in the Championship. This was competed by (Kintetsu Liners, Kobelco Steelers, Ricoh Black Rams, Yamaha Júbilo, NTT Communications Shining Arcs, Toyota Verblitz) and eventually taken by Kobe Steelers and Yamaha Júbilo.

Top Challenge One

In the 2011–12 Challenge series, the teams from Top Challenge One (Canon Eagles, Toyota Industries Shuttles, Kyushu Denryoku Voltex) and Kubota Spears (Top Challenge Two Winner) competed over 3 rounds to gain the first place (as Top Challenger One) for qualification to the Championship. This was eventually won by Canon Eagles.

University

In the 48th Japan National University Rugby Championship final Teikyo University defeated Tenri University 15–12. Both teams gained entry to the Championship as finalists.

Club

In the 19th All Japan Rugby Club Championship, Rokko Fighting Bull beat Tamariba Club to gain the Top Club side entry to the Championship.

First round

Quarter-final

Semi-final

Suntory Sungoliath and Sanyo Wild Knights bypassed the first two rounds into the semi-finals by reaching the final of the Top League playoffs in 2012.

Final