Toshiba Brave Lupus won the league by finishing on top of the round-robin competition.

• The top 4 teams also qualified to 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 (2004) knock out tournament, which was won by NEC Green Rockets.

IBM Big Blue and Toyota Verblitz won promotion to the 2004–05 Top League via the 2004 Top League Challenge Series, while Kyuden Voltex and Toyota Industries Shuttles progressed to the promotion play-offs.

Two promotion/relegation matches (Irekaesen) were played with the winners qualifying for the 2004–05 Top League.