| Pld | Pts | GD | ||
|---|---|---|---|---|
| 1 | Shimizu S-pulse | 38 | 82 | 30 |
| 2 | Yokohama FC | 38 | 76 | 33 |
| 3 | V-varen Nagasaki | 38 | 75 | 35 |
| 4 | Montedio Yamagata | 38 | 66 | 19 |
| 5 | Fagiano Okayama | 38 | 65 | 19 |
| 6 | Vegalta Sendai | 38 | 64 | 6 |
| 7 | JEF United Chiba | 38 | 61 | 19 |
| 8 | Tokushima Vortis | 38 | 55 | -2 |
| 9 | Iwaki | 38 | 54 | 12 |
| 10 | Blaublitz Akita | 38 | 54 | 1 |
| 11 | Renofa Yamaguchi | 38 | 53 | -1 |
| 12 | Roasso Kumamoto | 38 | 46 | -9 |
| 13 | Fujieda MYFC | 38 | 46 | -19 |
| 14 | Ventforet Kofu | 38 | 45 | -3 |
| 15 | Mito Hollyhock | 38 | 44 | -12 |
| 16 | Oita Trinita | 38 | 43 | -14 |
| 17 | Ehime FC | 38 | 40 | -28 |
| 18 | Tochigi SC | 38 | 34 | -24 |
| 19 | Kagoshima United | 38 | 30 | -24 |
| 20 | Thespakusatsu Gunma | 38 | 18 | -38 |