Time Zone – GMT-5 (America/New_York)
| Pl | W | D | L | Diff | Pts | |||
| 1 | V-Varen Nagasaki | 12 | 8 | 3 | 1 | 25:11 | 14 | 27 |
| 2 | Shimizu S-Pulse | 11 | 8 | 1 | 2 | 19:13 | 6 | 25 |
| 3 | Okayama | 11 | 6 | 4 | 1 | 14:7 | 7 | 22 |
| 4 | Yokohama FC | 11 | 5 | 3 | 3 | 16:8 | 8 | 18 |
| 5 | Kofu | 12 | 5 | 3 | 4 | 20:15 | 5 | 18 |
| 6 | Blaublitz | 11 | 5 | 3 | 3 | 12:8 | 4 | 18 |
| 7 | Ehime | 12 | 5 | 3 | 4 | 18:16 | 2 | 18 |
| 8 | Chiba | 12 | 5 | 2 | 5 | 25:15 | 10 | 17 |
| 9 | Vegalta Sendai | 12 | 4 | 5 | 3 | 12:11 | 1 | 17 |
| 10 | Iwaki | 11 | 4 | 4 | 3 | 20:10 | 10 | 16 |
| 11 | Montedio Yamagata | 11 | 5 | 1 | 5 | 12:12 | 0 | 16 |
| 12 | Renofa Yamaguchi | 11 | 4 | 3 | 4 | 14:9 | 5 | 15 |
| 13 | Oita Trinita | 11 | 3 | 4 | 4 | 10:11 | -1 | 13 |
| 14 | Kumamoto | 11 | 3 | 3 | 5 | 15:23 | -8 | 12 |
| 15 | Kagoshima Utd | 11 | 3 | 3 | 5 | 12:20 | -8 | 12 |
| 16 | Tochigi SC | 11 | 3 | 3 | 5 | 10:24 | -14 | 12 |
| 17 | Mito | 12 | 2 | 5 | 5 | 10:13 | -3 | 11 |
| 18 | Fujieda MYFC | 12 | 3 | 2 | 7 | 7:19 | -12 | 11 |
| 19 | Tokushima | 11 | 2 | 2 | 7 | 9:21 | -12 | 8 |
| 20 | Kusatsu | 12 | 1 | 3 | 8 | 7:21 | -14 | 6 |
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