The format was again changed from that used in 2001. In the First Stage all teams would play each other twice. The top three teams in each division would progress to the Upper Section, where each team would play each other twice.
The remaining seven sides would compete in the Lower Section, where once again they would only play each other once.
For the coming 2004 season, the league would be expanded to fourteen teams, in two divisions: L1, comprised of eight teams, and L2, which would comprise the remaining six.
The three bottom teams in the Lower Section in 2003 would play in L2. The top four teams would play another set of games, with each team playing the other three once. The top two teams resulting from this mini-tournament would play in L1, the bottom two in L2.
Tasaki Perule FC, who had been disappointed to finish second the previous two seasons, won their first and only league title. The club was disbanded at the end of the 2008 season.
First Stage - East Japan
Final Standings and Results
| Played | Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | YKK Tohoku LSC Flappers | 12 | 8 | 4 | 0 | 27 | 7 | 20 | 28 |
| 2 | Saitama Reinas | 12 | 8 | 4 | 0 | 28 | 9 | 19 | 28 |
| 3 | NTV Beleza | 12 | 8 | 3 | 1 | 47 | 6 | 41 | 27 |
| 4 | AS Elfen Sayama FC | 12 | 4 | 1 | 7 | 22 | 29 | -7 | 13 |
| 5 | Ohara Gakuen JaSRA SC | 12 | 3 | 2 | 7 | 18 | 23 | -5 | 11 |
| 6 | Shimizu Daihachi SC | 12 | 2 | 1 | 9 | 21 | 55 | -34 | 7 |
| 7 | JEF United Ichihara Ladies | 12 | 0 | 3 | 9 | 11 | 45 | -34 | 3 |
First Round, games played April 6th
Ohara Gakuen JaSRA SC 3 - 1 Shimizu Daihachi S. C.
Saitama Reinas 1 - 0 AS Elfen Sayama FC
JEF United Ichihara Ladies 0 - 9 NTV Beleza
Second Round, games played May 5th
Ohara Gakuen JaSRA SC 0 - 2 Saitama Reinas
AS Elfen Sayama FC 1 - 1 JEF United Ichihara Ladies
Shimizu Daihachi S. C. 0 - 5 YKK Tohoku Flappers
Third Round, games played May 11th
YKK Tohoku Flappers 1 - 1 JEF United Ichihara Ladies
NTV Beleza 4 - 1 Ohara Gakuen JaSRA SC
Shimizu Daihachi S. C. 3 - 5 Saitama Reinas
Fourth Round, games played May 18th
AS Elfen Sayama FC 1 - 2 NTV Beleza
Saitama Reinas 1 - 1 YKK Tohoku Flappers
JEF United Ichihara Ladies 0 - 2 Ohara Gakuen JaSRA SC
Fifth Round, games played May 25th
AS Elfen Sayama FC 0 - 1 YKK Tohoku Flappers
JEF United Ichihara Ladies 1 - 4 Saitama Reinas
NTV Beleza 9 - 0 Shimizu Daihachi S. C.
Sixth Round, games played June 1st
Ohara Gakuen JaSRA SC 2 - 3 AS Elfen Sayama FC
NTV Beleza 1 - 1 YKK Tohoku Flappers
Shimizu Daihachi S. C. 3 - 2 JEF United Ichihara Ladies
Seventh Round, games played June 8th
Shimizu Daihachi S. C. 1 - 4 AS Elfen Sayama FC
Saitama Reinas 1 - 1 NTV Beleza (played August 24th)
YKK Tohoku Flappers 2 - 0 Ohara Gakuen JaSRA SC (played September 7th)
Eighth Round, games played June 15th
AS Elfen Sayama FC 2 - 4 Ohara Gakuen JaSRA SC
JEF United Ichihara Ladies 3 - 5 Shimizu Daihachi S. C.
YKK Tohoku Flappers 2 - 0 NTV Beleza (played July 30th)
Ninth Round, games played June 22nd
Shimizu Daihachi S. C. 5 - 5 Ohara Gakuen JaSRA SC
NTV Beleza 7 - 0 JEF United Ichihara Ladies (played July 19th)
AS Elfen Sayama FC 0 - 3 Saitama Reinas
Tenth Round, games played June 29th
YKK Tohoku Flappers 2 - 0 AS Elfen Sayama FC
Shimizu Daihachi S. C. 0 - 3 NTV Beleza
Saitama Reinas 5 - 1 JEF United Ichihara Ladies
Eleventh Round, games played July 6th
JEF United Ichihara Ladies 0 - 2 AS Elfen Sayama FC
YKK Tohoku Flappers 4 - 1 Shimizu Daihachi S. C. (played August 31st)
Saitama Reinas 1 - 0 Ohara Gakuen JaSRA SC
Twelfth Round, games played July 13th
AS Elfen Sayama FC 9 - 2 Shimizu Daihachi S. C.
Ohara Gakuen JaSRA SC 0 - 1 YKK Tohoku Flappers (played August 24th)
September 07 NTV Beleza 0 - 0 Saitama Reinas
Thirteenth Round, games played August 3rd
Ohara Gakuen JaSRA SC 0 - 1 NTV Beleza
Saitama Reinas 3 - 0 Shimizu Daihachi S. C.
JEF United Ichihara Ladies 1 - 5 YKK Tohoku Flappers
Fourteenth Round, games played August 10th
Ohara Gakuen JaSRA SC 1 - 1 JEF United Ichihara Ladies
YKK Tohoku Flappers 2 - 2 Saitama Reinas
NTV Beleza 10 - 0 AS Elfen Sayama FC
First Stage - West Japan
Final Standings and Results
| Played | Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | Tasaki Perule FC | 10 | 10 | 0 | 0 | 56 | 4 | 52 | 30 |
| 2 | Iga FC Kunoichi | 10 | 6 | 2 | 2 | 41 | 8 | 33 | 20 |
| 3 | Speranza FC Takatsuki | 10 | 5 | 1 | 4 | 24 | 18 | 6 | 16 |
| 4 | Okayama Yunogo Belle | 10 | 5 | 0 | 5 | 24 | 24 | 0 | 15 |
| 5 | Takarazuka Bunnys Ladies | 10 | 2 | 1 | 7 | 14 | 27 | -13 | 7 |
| 6 | Renaissance Kumamoto FC | 10 | 0 | 0 | 10 | 3 | 81 | -78 | 0 |
First Round, games played May 11th
Okayama Yunogo Belle 4 - 2 Renaissance Kumamoto S.C.
Takarazuka Bunnys Ladies 1 - 1 Iga FC Kunoichi
Tasaki Perule FC 5 - 1 Speranza FC Takatsuki
Second Round, games played May 18th
Renaissance Kumamoto S.C. 0 - 11 Tasaki Perule FC
Iga FC Kunoichi 1 - 1 Speranza FC Takatsuki
Takarazuka Bunnys Ladies 1 - 5 Okayama Yunogo Belle
Third Round, games played May 25th
Iga FC Kunoichi 12 - 0 Renaissance Kumamoto S.C.
Speranza FC Takatsuki 1 - 0 Takarazuka Bunnys Ladies
Tasaki Perule FC 3 - 0 Okayama Yunogo Belle
Fourth Round, games played June 1st
Speranza FC Takatsuki 6 - 0 Renaissance Kumamoto S.C.
Tasaki Perule FC 5 - 0 Takarazuka Bunnys Ladies
Okayama Yunogo Belle 0 - 2 Iga FC Kunoichi
Fifth Round, games played June 8th
Takarazuka Bunnys Ladies 4 - 0 Renaissance Kumamoto S.C.
Iga FC Kunoichi 0 - 4 Tasaki Perule FC (played July 19th)
Okayama Yunogo Belle 0 - 3 Speranza FC Takatsuki
Sixth Round, games played August 3rd
Speranza FC Takatsuki 1 - 5 Tasaki Perule FC
Iga FC Kunoichi 1 - 0 Takarazuka Bunnys Ladies
Renaissance Kumamoto S.C. 0 - 7 Okayama Yunogo Belle
Seventh Round, games played August 10th
Tasaki Perule FC 10 - 0 Renaissance Kumamoto S.C.
Speranza FC Takatsuki 1 - 2 Iga FC Kunoichi
Okayama Yunogo Belle 2 - 1 Takarazuka Bunnys Ladies
Eighth Round, games played June 29th
Renaissance Kumamoto S.C. 0 - 15 Iga FC Kunoichi
Takarazuka Bunnys Ladies 1 - 2 Speranza FC Takatsuki
Okayama Yunogo Belle 2 - 5 Tasaki Perule FC
Ninth Round, games played July 6th
Renaissance Kumamoto S.C. 0 - 6 Speranza FC Takatsuki
Iga FC Kunoichi 5 - 0 Okayama Yunogo Belle (played August 24th)
Takarazuka Bunnys Ladies 0 - 7 Tasaki Perule FC (played September 7th)
Tenth Round, games played July 13th
Renaissance Kumamoto S.C. 1 - 6 Takarazuka Bunnys Ladies
Tasaki Perule FC 1 - 0 Iga FC Kunoichi (played August 31st)
Speranza FC Takatsuki 2 - 4 Okayama Yunogo Belle (played September 7th)
Second Stage - Upper Section
Final Standings and Results
| Played | Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | Tasaki Perule FC | 10 | 8 | 1 | 1 | 31 | 7 | 24 | 25 |
| 2 | NTV Beleza | 10 | 6 | 1 | 3 | 15 | 7 | 8 | 19 |
| 3 | Iga FC Kunoichi | 10 | 6 | 0 | 4 | 20 | 11 | 9 | 18 |
| 4 | Saitama Reinas | 10 | 5 | 1 | 4 | 13 | 13 | 0 | 16 |
| 5 | YKK Tohoku LSC Flappers | 10 | 2 | 0 | 8 | 8 | 24 | -16 | 6 |
| 6 | Speranza FC Takatsuki | 10 | 1 | 1 | 8 | 4 | 29 | -25 | 4 |
First Round, games played October 19th
YKK Tohoku Flappers 0 - 2 Iga FC Kunoichi
NTV Beleza 4 - 0 Speranza FC Takatsuki
Tasaki Perule FC 4 - 0 Saitama Reinas
Second Round, games played October 25th
Tasaki Perule FC 2 - 0 Iga FC Kunoichi
YKK Tohoku Flappers 0 - 3 NTV Beleza
Saitama Reinas 1 - 1 Speranza FC Takatsuki
Third Round, games played November 2nd
Iga FC Kunoichi 2 - 0 Saitama Reinas
YKK Tohoku Flappers 0 - 2 Speranza FC Takatsuki
NTV Beleza 2 - 1 Tasaki Perule FC
Fourth Round, games played November 9th
YKK Tohoku Flappers 0 - 4 Saitama Reinas
Iga FC Kunoichi 2 - 0 NTV Beleza
Speranza FC Takatsuki 0 - 8 Tasaki Perule FC
Fifth Round, games played November 16th
Tasaki Perule FC 4 - 1 YKK Tohoku Flappers
Speranza FC Takatsuki 0 - 4 Iga FC Kunoichi
Saitama Reinas 0 - 1 NTV Beleza
Sixth Round, games played November 23rd
Saitama Reinas 1 - 2 Tasaki Perule FC
Iga FC Kunoichi 3 - 2 YKK Tohoku Flappers
Speranza FC Takatsuki 0 - 3 NTV Beleza
Seventh Round, games played November 30th
NTV Beleza 0 - 1 YKK Tohoku Flappers
Iga FC Kunoichi 2 - 3 Tasaki Perule FC
Speranza FC Takatsuki 0 - 1 Saitama Reinas
Eighth Round, games played December 7th
Tasaki Perule FC 0 - 0 NTV Beleza
Saitama Reinas 0 - 2 Iga FC Kunoichi
Speranza FC Takatsuki 1 - 0 YKK Tohoku Flappers
Ninth Round, games played December 14th
NTV Beleza 2 - 0 Iga FC Kunoichi
Tasaki Perule FC 3 - 0 Speranza FC Takatsuki
Saitama Reinas 2 - 1 YKK Tohoku Flappers
Tenth Round, games played December 20th and 21st
Iga FC Kunoichi 5 - 1 Speranza FC Takatsuki
NTV Beleza 2 - 3 Saitama Reinas Saitama Reinas
YKK Tohoku Flappers 1 - 4 Tasaki Perule FC
Second Stage - Lower Section
Final Standings and Results
| Played | Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 7 | Ohara Gakuen JaSRA SC | 6 | 5 | 1 | 0 | 21 | 3 | 18 | 16 |
| 8 | Okayama Yunogo Belle | 6 | 4 | 2 | 0 | 24 | 5 | 19 | 14 |
| 9 | Takarazuka Bunnys Ladies | 6 | 4 | 1 | 1 | 13 | 7 | 6 | 13 |
| 10 | AS Elfen Sayama FC | 6 | 2 | 0 | 4 | 10 | 16 | -6 | 6 |
| 11 | Shimizu Daihachi SC | 6 | 2 | 0 | 4 | 7 | 14 | -7 | 6 |
| 12 | JEF United Ichihara Ladies | 6 | 2 | 0 | 4 | 9 | 22 | -13 | 6 |
| 13 | Renaissance Kumamoto FC | 6 | 0 | 0 | 6 | 4 | 21 | -17 | 0 |
First Round, games played October 19th
AS Elfen Sayama FC 3 - 2 Renaissance Kumamoto S.C.
Ohara Gakuen JaSRA SC 4 - 0 Takarazuka Bunnys Ladies
Okayama Yunogo Belle 2 - 0 Shimizu Daihachi S. C.
Second Round, games played October 26th
Shimizu Daihachi S. C. 2 - 0 Renaissance Kumamoto S.C.
Takarazuka Bunnys Ladies 5 - 1 JEF United Ichihara Ladies
Ohara Gakuen JaSRA SC 5 - 0 AS Elfen Sayama FC
Third Round, games played November 2nd
Renaissance Kumamoto S.C. 1 - 5 Okayama Yunogo Belle
Shimizu Daihachi S. C. 2 - 5 Ohara Gakuen JaSRA SC
JEF United Ichihara Ladies 4 - 3 AS Elfen Sayama FC
Fourth Round, games played November 9th
Takarazuka Bunnys Ladies 3 - 3 Okayama Yunogo Belle
Shimizu Daihachi S. C. 0 - 3 AS Elfen Sayama FC
Renaissance Kumamoto S.C. 1 - 3 JEF United Ichihara Ladies
Fifth Round, games played November 16th
AS Elfen Sayama FC 1 - 2 Takarazuka Bunnys Ladies
JEF United Ichihara Ladies 1 - 3 Shimizu Daihachi S. C.
Okayama Yunogo Belle 1 - 1 Ohara Gakuen JaSRA SC
Sixth Round, games played November 23rd
Ohara Gakuen JaSRA SC 6 - 0 Renaissance Kumamoto S.C.
Takarazuka Bunnys Ladies 1 - 0 Shimizu Daihachi S. C.
Okayama Yunogo Belle 8 - 0 JEF United Ichihara Ladies
Seventh Round, games played November 30th
AS Elfen Sayama FC 0 - 3 Okayama Yunogo Belle
Renaissance Kumamoto S.C. 0 - 2 Takarazuka Bunnys Ladies
JEF United Ichihara Ladies 0 - 2 Ohara Gakuen JaSRA SC
Promotion/Relegation Series
First Round, games played December 14th
Okayama Yunogo Belle 1 - 2 Takarazuka Bunnys Ladies
Ohara Gakuen JaSRA SC 1 - 2 AS Elfen Sayama FC
First Round, games played December 20th
Takarazuka Bunnys Ladies 0 - 1 Ohara Gakuen JaSRA SC
Okayama Yunogo Belle 5 - 2 AS Elfen Sayama FC
First Round, games played December 23rd
Ohara Gakuen JaSRA SC 4 - 3 Okayama Yunogo Belle
AS Elfen Sayama FC 0 - 1 Takarazuka Bunnys Ladies
| Played | Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | Ohara Gakuen JaSRA SC | 3 | 2 | 0 | 1 | 6 | 5 | 1 | 6 |
| 2 | Takarazuka Bunnys Ladies | 3 | 2 | 0 | 1 | 3 | 2 | 1 | 6 |
| 3 | Okayama Yunogo Belle | 3 | 1 | 0 | 2 | 9 | 8 | 1 | 3 |
| 4 | AS Elfen Sayama FC | 3 | 1 | 0 | 2 | 4 | 7 | -3 | 3 |
Ohara Gakuen JaSRA SC and Takarazuka Bunnys Ladies will play the 2004 season in L1. Okayama Yunogo Belle and AS Elfen Sayama FC will play the 2004 season in L2.