OKI FC Winds withdrew from the league at the end of the season and closed its doors, while the Nippon Sport Science University withdrew from league football. They later rejoined the newly formed Challenge League in 2010, and are called Nittaidai FC Ladies.
The league abandoned its extra time and penalties system, and returned to a points system (three for a win, one for a draw and none for a loss). The 1999 season ran from July 18th until December 12th.
Yomiuri Beleza were renamed as NTV Beleza.
First Stage Final Standings and Results
| Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | Prima Ham FC Kunoichi | 5 | 1 | 1 | 37 | 3 | 34 | 16 |
| 2 | Tasaki Perule FC | 5 | 1 | 1 | 18 | 4 | 14 | 16 |
| 3 | NTV Beleza | 5 | 0 | 2 | 32 | 9 | 23 | 15 |
| 4 | Matsushita Denki Panasonic Bambina | 4 | 1 | 2 | 20 | 6 | 14 | 13 |
| 5 | OKI FC Winds | 4 | 1 | 2 | 14 | 11 | 3 | 13 |
| 6 | Takarazuka Bunnys Ladies | 2 | 0 | 5 | 11 | 19 | -8 | 6 |
| 7 | Nippon Sport Science University | 1 | 0 | 6 | 5 | 47 | -42 | 3 |
| 8 | Urawa Reinas | 0 | 0 | 7 | 2 | 40 | -38 | 0 |
First Round, games played July 18th
Takarazuka Bunnys Ladies 1 - 2 Matsushita Denki Panasonic Bambina
Urawa Reinas 1 - 4 Nippon Sport Science University
NTV Beleza 2 - 1 OKI FC Winds
Prima Ham FC Kunoichi 0 - 1 Tasaki Perule FC
Second Round, games played July 25th
Matsushita Denki Panasonic Bambina 0 - 0 Prima Ham FC Kunoichi
Tasaki Perule FC 2 - 2 OKI FC Winds
Takarazuka Bunnys Ladies 4 - 1 Nippon Sport Science University
Urawa Reinas 0 - 12 NTV Beleza
Third Round, games played August 1st
Urawa Reinas 0 - 2 Tasaki Perule FC
Nippon Sport Science University 0 - 8 NTV Beleza
OKI FC Winds 3 - 0 Matsushita Denki Panasonic Bambina
Prima Ham FC Kunoichi 5 - 0 Takarazuka Bunnys Ladies
Fourth Round, games played August 8th
Tasaki Perule FC 2 - 1 NTV Beleza
Takarazuka Bunnys Ladies 0 - 2 OKI FC Winds
Matsushita Denki Panasonic Bambina 4 - 0 Urawa Reinas
Prima Ham FC Kunoichi 11 - 0 Nippon Sport Science University
Fifth Round, games played September 4th and 5th
Nippon Sport Science University 0 - 8 Tasaki Perule FC
Urawa Reinas 0 - 5 Takarazuka Bunnys Ladies
OKI FC Winds 1 - 6 Prima Ham FC Kunoichi
NTV Beleza 2 - 1 Matsushita Denki Panasonic Bambina
Sixth Round, games played September 11th and 12th
OKI FC Winds 3 - 0 Nippon Sport Science University
Matsushita Denki Panasonic Bambina 1 - 0 Tasaki Perule FC
Takarazuka Bunnys Ladies 1 - 6 NTV Beleza
Prima Ham FC Kunoichi 11 - 0 Urawa Reinas
Seventh Round, games played September 19th
Matsushita Denki Panasonic Bambina 12 - 0 Nippon Sport Science University
Takarazuka Bunnys Ladies 0 - 3 Tasaki Perule FC
Urawa Reinas 1 - 2 OKI FC Winds
Prima Ham FC Kunoichi 4 - 1 NTV Beleza
Second Stage Final Standings and Results
| Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | NTV Beleza | 5 | 2 | 0 | 20 | 4 | 16 | 17 |
| 2 | Tasaki Perule FC | 5 | 1 | 1 | 16 | 5 | 11 | 16 |
| 3 | Prima Ham FC Kunoichi | 5 | 0 | 2 | 22 | 6 | 16 | 15 |
| 4 | OKI FC Winds | 4 | 1 | 2 | 19 | 7 | 12 | 13 |
| 5 | Matsushita Denki Panasonic Bambina | 3 | 0 | 4 | 17 | 9 | 8 | 9 |
| 6 | Takarazuka Bunnys Ladies | 3 | 0 | 4 | 10 | 9 | 1 | 9 |
| 7 | Urawa Reinas | 1 | 0 | 6 | 6 | 26 | -20 | 3 |
| 8 | Nippon Sport Science University | 0 | 0 | 7 | 3 | 47 | -44 | 0 |
First Round, games played October 2nd and 3rd
Nippon Sport Science University 1 - 4 Urawa Reinas
Tasaki Perule FC 0 - 1 Prima Ham FC Kunoichi
Matsushita Denki Panasonic Bambina 0 - 1 Takarazuka Bunnys Ladies
OKI FC Winds 1 - 1 NTV Beleza
Second Round, games played October 9th and 11th
OKI FC Winds 0 - 2 Tasaki Perule FC
Nippon Sport Science University 0 - 5 Takarazuka Bunnys Ladies
NTV Beleza 5 - 0 Urawa Reinas
Prima Ham FC Kunoichi 0 - 1 Matsushita Denki Panasonic Bambina
Third Round, games played October 17th
Takarazuka Bunnys Ladies 2 - 3 Prima Ham FC Kunoichi
Matsushita Denki Panasonic Bambina 0 - 2 OKI FC Winds
Tasaki Perule FC 3 - 0 Urawa Reinas
NTV Beleza 7 - 0 Nippon Sport Science University
Fourth Round, games played October 31st
NTV Beleza 2 - 2 Tasaki Perule FC
OKI FC Winds 2 - 0 Takarazuka Bunnys Ladies
Urawa Reinas 1 - 5 Matsushita Denki Panasonic Bambina (played November 3rd)
Nippon Sport Science University 1 - 12 Prima Ham FC Kunoichi
Fifth Round, games played November 28th
Takarazuka Bunnys Ladies 2 - 0 Urawa Reinas
Matsushita Denki Panasonic Bambina 1 - 3 NTV Beleza
Tasaki Perule FC 4 - 1 Nippon Sport Science University
Prima Ham FC Kunoichi 3 - 1 OKI FC Winds
Sixth Round, games played December 5th
Urawa Reinas 0 - 3 Prima Ham FC Kunoichi
Nippon Sport Science University 0 - 6 OKI FC Winds
Tasaki Perule FC 2 - 1 Matsushita Denki Panasonic Bambina
NTV Beleza 1 - 0 Takarazuka Bunnys Ladies
Seventh Round, games played December 12th
Tasaki Perule FC 3 - 0 Takarazuka Bunnys Ladies
Nippon Sport Science University 0 - 9 Matsushita Denki Panasonic Bambina
NTV Beleza 1 - 0 Prima Ham FC Kunoichi
OKI FC Winds 7 - 1 Urawa Reinas
The final deciding match for the championship was played on December 19th, 1999. Prima Ham FC Kunoichi won their second title, and this was their most recent championship victory (as of 2014 they are called Iga FC Kunoichi).
Championship Deciding Match:
NTV Beleza 1 - 3 Prima Ham FC Kunoichi
The overall final standings are shown below. Regardless of the number of points gained during the season, the first placed team is the winner of the championship with the loser occupying the second position. The remaining positions are determined by ranking the teams by number of points, goal difference etc.
Overall Final Standings
| Won | Drawn | Lost | GF | GA | +/- | Points | ||
| 1 | Prima Ham FC Kunoichi | 10 | 1 | 3 | 59 | 9 | 50 | 31 |
| 2 | NTV Beleza | 10 | 2 | 2 | 52 | 13 | 39 | 32 |
| 3 | Tasaki Perule FC | 10 | 2 | 2 | 34 | 9 | 25 | 32 |
| 4 | OKI FC Winds | 8 | 2 | 4 | 33 | 18 | 15 | 26 |
| 5 | Matsushita Denki Panasonic Bambina | 7 | 1 | 6 | 37 | 15 | 22 | 22 |
| 6 | Takarazuka Bunnys Ladies | 5 | 0 | 9 | 21 | 28 | -7 | 15 |
| 7 | Urawa Reinas | 1 | 0 | 13 | 8 | 66 | -58 | 3 |
| 8 | Nippon Sport Science University | 1 | 0 | 13 | 8 | 94 | -86 | 3 |
