Each team played the opposition sides twice within their own division, with the same points format as in 1999. Following the first stage, the top two teams in each division would form a new Upper Section division, with the remaining five teams forming the Lower Section. The teams in the Upper Section would play each other twice, those in the Lower Section just once.
Matsushita and Prima Ham both withdrew sponsorship from their respective teams, and so they became community based instead.
Therefore Matsushita Denki Panasonic Bambina was renamed Speranza FC Takatsuki and Prima Ham FC Kunoichi was renamed Iga FC Kunoichi.
NTV Beleza won the title for the fifth time, having last won the championship in 1993.
First Stage - East Japan
Final Standings and Results
| Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | NTV Beleza | 5 | 1 | 0 | 25 | 1 | 24 | 16 |
| 2 | YKK Tohoku LSC Flappers | 3 | 2 | 1 | 22 | 6 | 16 | 11 |
| 3 | Urawa Reinas | 1 | 2 | 3 | 4 | 13 | -9 | 5 |
| 4 | JEF United Ichihara Ladies | 0 | 1 | 5 | 2 | 33 | -31 | 1 |
First Round, games played July 2nd
YKK Tohoku Flappers 0 - 3 NTV Beleza
JEF United Ichihara Ladies 0 - 2 Urawa Reinas
Second Round, games played July 9th
Urawa Reinas 0 - 0 YKK Tohoku Flappers
NTV Beleza 10 - 0 JEF United Ichihara Ladies
Third Round, games played July 16th
YKK Tohoku Flappers 7 - 1 JEF United Ichihara Ladies
Urawa Reinas 0 - 2 NTV Beleza
Fourth Round, games played September 3rd
NTV Beleza 1 - 1 YKK Tohoku Flappers
Urawa Reinas 1 - 1 JEF United Ichihara Ladies
Fifth Round, games played September 10th
YKK Tohoku Flappers 6 - 1 Urawa Reinas
JEF United Ichihara Ladies 0 - 5 NTV Beleza
Sixth Round, games played September 24th
JEF United Ichihara Ladies 0 - 8 YKK Tohoku Flappers
NTV Beleza 4 - 0 Urawa Reinas
First Stage - West Japan
Final Standings and Results
| Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | Tasaki Perule FC | 7 | 0 | 1 | 51 | 6 | 45 | 21 |
| 2 | Iga FC Kunoichi | 6 | 1 | 1 | 43 | 5 | 38 | 19 |
| 3 | Speranza FC Takatsuki | 3 | 2 | 3 | 19 | 6 | 13 | 11 |
| 4 | Takarazuka Bunnys Ladies | 2 | 1 | 5 | 9 | 23 | -14 | 7 |
| 5 | Renaissance Kumamoto FC | 0 | 0 | 8 | 1 | 83 | -82 | 0 |
First Round, games played July 1st and 2nd
Takarazuka Bunnys Ladies 0 - 7 Iga FC Kunoichi
Speranza FC Takatsuki 0 - 1 Tasaki Perule FC
Second Round, games played July 9th
Tasaki Perule FC 4 - 1 Takarazuka Bunnys Ladies
Renaissance Kumamoto S.C. 0 - 15 Iga FC Kunoichi
Third Round, games played July 16th
Speranza FC Takatsuki 3 - 0 Takarazuka Bunnys Ladies
Renaissance Kumamoto S.C. 0 - 18 Tasaki Perule FC
Fourth Round, games played July 23rd
Speranza FC Takatsuki 1 - 2 Iga FC Kunoichi
Takarazuka Bunnys Ladies 5 - 0 Renaissance Kumamoto S.C.
Fifth Round, games played July 30th
Speranza FC Takatsuki 5 - 0 Renaissance Kumamoto S.C.
Tasaki Perule FC 2 - 1 Iga FC Kunoichi
Sixth Round, games played September 3rd
Tasaki Perule FC 1 - 0 Speranza FC Takatsuki
Iga FC Kunoichi 2 - 0 Takarazuka Bunnys Ladies
Seventh Round, games played September 10th
Takarazuka Bunnys Ladies 0 - 7 Tasaki Perule FC
Iga FC Kunoichi 11 - 0 Renaissance Kumamoto S.C.
Eighth Round, games played September 17th
Takarazuka Bunnys Ladies 0 - 0 Speranza FC Takatsuki
Renaissance Kumamoto S.C. 0 - 17 Tasaki Perule FC
Ninth Round, games played September 24th
Iga FC Kunoichi 1 - 1 Speranza FC Takatsuki
Takarazuka Bunnys Ladies 3 - 0 Renaissance Kumamoto S.C.
Tenth Round, games played October 1st
Renaissance Kumamoto S.C. 1 - 9 Speranza FC Takatsuki
Iga FC Kunoichi 4 - 1 Tasaki Perule FC
Second Stage - Upper Section
Final Standings and Results
| Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | NTV Beleza | 4 | 2 | 0 | 9 | 3 | 6 | 14 |
| 2 | Iga FC Kunoichi | 2 | 2 | 2 | 8 | 7 | 1 | 8 |
| 3 | Tasaki Perule FC | 0 | 4 | 2 | 7 | 10 | -3 | 4 |
| 4 | YKK Tohoku LSC Flappers | 0 | 4 | 2 | 4 | 8 | -4 | 4 |
First Round, games played November 5th
Tasaki Perule FC 0 - 0 YKK Tohoku Flappers
Iga FC Kunoichi 0 - 1 NTV Beleza
Second Round, games played November 12th
Tasaki Perule FC 2 - 2 Iga FC Kunoichi
NTV Beleza 1 - 0 YKK Tohoku Flappers
Third Round, games played November 19th
Iga FC Kunoichi 3 - 0 YKK Tohoku Flappers
Tasaki Perule FC 2 - 2 NTV Beleza
Fourth Round, games played November 26th
YKK Tohoku Flappers 0 - 0 Tasaki Perule FC
NTV Beleza 2 - 0 Iga FC Kunoichi
Fifth Round, games played December 3rd
YKK Tohoku Flappers 1 - 1 NTV Beleza
Iga FC Kunoichi 2 - 1 Tasaki Perule FC
Sixth Round, games played December 9th
YKK Tohoku Flappers 1 - 1 Iga FC Kunoichi
NTV Beleza 2 - 0 Tasaki Perule FC
Second Stage - Lower Section
Final Standings and Results
| Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 5 | Speranza FC Takatsuki | 4 | 0 | 0 | 19 | 3 | 16 | 12 |
| 6 | Urawa Reinas | 3 | 0 | 1 | 20 | 3 | 17 | 9 |
| 7 | Takarazuka Bunnys Ladies | 2 | 0 | 2 | 10 | 9 | 1 | 6 |
| 8 | JEF United Ichihara Ladies | 1 | 0 | 3 | 3 | 14 | -11 | 3 |
| 9 | Renaissance Kumamoto FC | 0 | 0 | 4 | 0 | 23 | -23 | 0 |
First Round, games played November 5th
Renaissance Kumamoto S.C. 0 - 5 Urawa Reinas
Takarazuka Bunnys Ladies 2 - 1 JEF United Ichihara Ladies
Second Round, games played November 12th
Takarazuka Bunnys Ladies 6 - 0 Renaissance Kumamoto S.C.
Speranza FC Takatsuki 2 - 0 JEF United Ichihara Ladies
Third Round, games played November 19th
Urawa Reinas 4 - 0 Takarazuka Bunnys Ladies
Speranza FC Takatsuki 10 - 0 Renaissance Kumamoto S.C.
Fourth Round, games played November 26th
Urawa Reinas 10 - 0 JEF United Ichihara Ladies
Speranza FC Takatsuki 4 - 2 Takarazuka Bunnys Ladies
Fifth Round, games played December 3rd
Urawa Reinas 1 - 3 Speranza FC Takatsuki
JEF United Ichihara Ladies 2 - 0 Renaissance Kumamoto S.C.
