[1] Toshiba Brave Lupus won both the league round-robin and the Microsoft Cup knockout competitions.

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

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 • Number of matches won excluding the first match, then the second and so on until the tie is settled The top eight teams in the league played off for the Microsoft Cup (2006) knock out tournament, which was won by Toshiba Brave Lupus.

Coca-Cola West Red Sparks and IBM Big Blue won promotion to the 2006–07 Top League via the 2006 Top League Challenge Series, while Honda Heat, Kintetsu Liners, Kyuden Voltex and NTT Communications Shining Arcs progressed to the promotion play-offs.

So Fukuoka, Ricoh, Secom, and World all remained in the Top League for 2006–07.