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| Player | Team | Goals |
|---|---|---|
| M. Oguro | Kyoto Sanga | 27 |
| Wellington Sousa | Shonan Bellmare | 20 |
| T. Funayama | Matsumoto Yamaga | 19 |
| C. Nazarit | FC Gifu | 17 |
| R. Maeda | Jubilo Iwata | 17 |
| Diego Souza | Montedio Yamagata | 15 |
| T. Ikemoto | Kitakyushu | 15 |
| Daniel Lovinho | Thespakusatsu Gunma | 14 |
| K. Tokura | Consadole Sapporo | 14 |
| S. Okada | Shonan Bellmare | 14 |
| Kempes | JEF United Chiba | 13 |
| K. Kawahara | Ehime FC | 13 |
| H. Namba | FC Gifu | 12 |
| K. Sato | V-varen Nagasaki | 12 |
| M. Yoshida | Mito Hollyhock | 11 |
| Y. Oshitani | Fagiano Okayama | 11 |
| G. Nishida | Ehime FC | 10 |
| T. Morimoto | JEF United Chiba | 10 |
| H. Jogo | Avispa Fukuoka | 9 |
| K. Taketomi | Shonan Bellmare | 9 |
| R. Yamazaki | Jubilo Iwata | 9 |
| T. Kanamori | Avispa Fukuoka | 9 |
| T. Okubo | Tochigi SC | 9 |
| T. Sawada | Roasso Kumamoto | 9 |
| K. Mitsuhira | Kyoto Sanga | 8 |
| M. Miyasaka | Montedio Yamagata | 8 |
| T. Kokeguchi | Kataller Toyama | 8 |
| Y. Horigome | Ehime FC | 8 |
| Y. Iwakami | Matsumoto Yamaga | 8 |
| D. Kikuchi | Shonan Bellmare | 7 |