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| Player | Team | Goals |
|---|---|---|
| Kempes | JEF United Chiba | 22 |
| T. Usami | Gamba Osaka | 19 |
| Y. Uchimura | Consadole Sapporo | 17 |
| Cristiano | Tochigi SC | 16 |
| K. Ogawa | Vissel Kobe | 16 |
| Popo | Vissel Kobe | 16 |
| Sabia | Tochigi SC | 16 |
| T. Tsuda | Tokushima Vortis | 15 |
| Douglas | Tokushima Vortis | 13 |
| Leandro | Gamba Osaka | 13 |
| R. Hirashige | Thespakusatsu Gunma | 13 |
| K. Hara | Kyoto Sanga | 12 |
| K. Hashimoto | Mito Hollyhock | 12 |
| K. Sato | V-varen Nagasaki | 12 |
| R. Hayashi | Montedio Yamagata | 12 |
| T. Okubo | Yokohama FC | 12 |
| Y. Nakashima | Montedio Yamagata | 12 |
| D. Ishizu | Avispa Fukuoka | 11 |
| D. Sakata | Avispa Fukuoka | 11 |
| N. Takahara | Tokyo Verdy | 11 |
| S. Yokotani | Kyoto Sanga | 11 |
| T. Funayama | Matsumoto Yamaga | 11 |
| T. Suzuki | Mito Hollyhock | 11 |
| G. Nagasato | Gainare Tottori | 10 |
| K. Someya | FC Gifu | 10 |
| Mazinho | Vissel Kobe | 10 |
| S. Shiozawa | Matsumoto Yamaga | 10 |
| T. Kokeguchi | Kataller Toyama | 10 |
| Adi | Gamba Osaka | 9 |
| M. Kato | Ehime FC | 9 |