| Standings | P | W | D | L | GD | PTS | |
|---|---|---|---|---|---|---|---|
| 1 | Mito Hollyhock | 36 | 19 | 10 | 7 | 20 | 67 |
| 2 | V-Varen Nagasaki | 36 | 18 | 12 | 6 | 18 | 66 |
| 3 | Omiya Ardija | 36 | 18 | 9 | 9 | 23 | 63 |
| 4 | JEF United Chiba | 36 | 18 | 9 | 9 | 16 | 63 |
| 5 | Tokushima Vortis | 36 | 17 | 10 | 9 | 20 | 61 |
| 6 | Vegalta Sendai | 36 | 16 | 13 | 7 | 12 | 61 |
| 7 | Jubilo Iwata | 36 | 18 | 6 | 12 | 7 | 60 |
| 8 | Sagan Tosu | 36 | 16 | 9 | 11 | 4 | 57 |
| 9 | Iwaki SC | 36 | 14 | 10 | 12 | 10 | 52 |
| 10 | Imabari | 36 | 13 | 13 | 10 | 5 | 52 |
| 11 | Montedio Yamagata | 36 | 14 | 7 | 15 | 3 | 49 |
| 12 | Hokkaido Consadole Sapporo | 36 | 15 | 4 | 17 | -16 | 49 |
| 13 | Ventforet Kofu | 36 | 11 | 10 | 15 | -7 | 43 |
| 14 | Blaublitz Akita | 36 | 11 | 9 | 16 | -13 | 42 |
| 15 | Fujieda MYFC | 36 | 9 | 11 | 16 | -8 | 38 |
| 16 | Oita Trinita | 36 | 8 | 14 | 14 | -14 | 38 |
| 17 | Roasso Kumamoto | 36 | 9 | 8 | 19 | -16 | 35 |
| 18 | Renofa Yamaguchi | 36 | 6 | 14 | 16 | -12 | 32 |
| 19 | Kataller Toyama | 36 | 7 | 10 | 19 | -19 | 31 |
| 20 | Ehime FC | 36 | 3 | 12 | 21 | -33 | 21 |