The 2003–04 Top League was the first season of Japan's domestic rugby union competition, the Top League. Toshiba Brave Lupus won the league by finishing on top of the round-robin competition.
Toshiba Brave Lupus lost the final of Microsoft Cup to NEC Green Rockets, but the cup was considered a separate competition to the Top League prior to 2007.
Four points for a win, two for a draw, one bonus point for four tries or more (BP1) and one bonus point for losing by seven or less (BP2).
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
Two promotion/relegation matches (Irekaesen) were played with the winners qualifying for the 2004–05 Top League. The 10th-placed team from the Top League against the 3rd-placed team from Challenge 1. The 9th-placed team from the Top League against the 1st-placed team from Challenge 2.