| # | Équipe | J | G | N | P | BP/BC | Pts |
|---|---|---|---|---|---|---|---|
| 1 | Mito Hollyhock | 35 | 19 | 10 | 6 | 52-30 | 67 |
| 2 | V-Varen Nagasaki | 35 | 17 | 12 | 6 | 56-42 | 63 |
| 3 | JEF United Ichihara | 35 | 18 | 8 | 9 | 49-33 | 62 |
| 4 | Omiya Ardija | 35 | 17 | 9 | 9 | 55-34 | 60 |
| 5 | Vegalta Sendai | 35 | 15 | 13 | 7 | 45-35 | 58 |
| 6 | Tokushima Vortis | 35 | 16 | 10 | 9 | 38-21 | 58 |
| 7 | Júbilo Iwata | 35 | 17 | 6 | 12 | 53-47 | 57 |
| 8 | Sagan Tosu | 35 | 16 | 9 | 10 | 44-38 | 57 |
| 9 | Iwaki FC | 35 | 14 | 10 | 11 | 54-42 | 52 |
| 10 | FC Imabari | 35 | 13 | 13 | 9 | 44-38 | 52 |
| 11 | Consadole Sapporo | 35 | 14 | 4 | 17 | 43-61 | 46 |
| 12 | Montedio Yamagata | 35 | 13 | 7 | 15 | 52-50 | 46 |
| 13 | Ventforet Kofu | 35 | 11 | 10 | 14 | 36-40 | 43 |
| 14 | Blaublitz Akita | 35 | 10 | 9 | 16 | 40-55 | 39 |
| 15 | Oita Trinita | 35 | 8 | 14 | 13 | 26-38 | 38 |
| 16 | Fujieda MYFC | 35 | 9 | 10 | 16 | 39-47 | 37 |
| 17 | Roasso Kumamoto | 35 | 9 | 8 | 18 | 40-54 | 35 |
| 18 | Renofa Yamaguchi | 35 | 6 | 14 | 15 | 32-43 | 32 |
| 19 | Kataller Toyama | 35 | 6 | 10 | 19 | 26-47 | 28 |
| 20 | Ehime FC | 35 | 3 | 12 | 20 | 34-63 | 21 |