Time Zone – GMT-5 (America/New_York)
| Pl | W | D | L | Diff | Pts | |||
| 1 | Shimizu S-Pulse | 24 | 17 | 1 | 6 | 42:26 | 16 | 52 |
| 2 | V-Varen Nagasaki | 24 | 14 | 9 | 1 | 47:22 | 25 | 51 |
| 3 | Yokohama FC | 24 | 15 | 5 | 4 | 42:14 | 28 | 50 |
| 4 | Okayama | 24 | 11 | 8 | 5 | 31:20 | 11 | 41 |
| 5 | Renofa Yamaguchi | 24 | 11 | 5 | 8 | 28:20 | 8 | 38 |
| 6 | Vegalta Sendai | 24 | 10 | 8 | 6 | 29:29 | 0 | 38 |
| 7 | Chiba | 24 | 11 | 3 | 10 | 43:29 | 14 | 36 |
| 8 | Iwaki | 24 | 9 | 7 | 8 | 33:25 | 8 | 34 |
| 9 | Ehime | 24 | 9 | 7 | 8 | 29:36 | -7 | 34 |
| 10 | Tokushima | 24 | 9 | 5 | 10 | 26:32 | -6 | 32 |
| 11 | Blaublitz | 24 | 8 | 7 | 9 | 24:24 | 0 | 31 |
| 12 | Fujieda MYFC | 24 | 9 | 3 | 12 | 21:33 | -12 | 30 |
| 13 | Montedio Yamagata | 24 | 8 | 5 | 11 | 23:26 | -3 | 29 |
| 14 | Oita Trinita | 24 | 6 | 10 | 8 | 19:25 | -6 | 28 |
| 15 | Kumamoto | 24 | 7 | 6 | 11 | 30:41 | -11 | 27 |
| 16 | Kofu | 24 | 6 | 8 | 10 | 34:36 | -2 | 26 |
| 17 | Mito | 24 | 5 | 8 | 11 | 22:29 | -7 | 23 |
| 18 | Kagoshima Utd | 24 | 5 | 8 | 11 | 23:38 | -15 | 23 |
| 19 | Tochigi SC | 24 | 5 | 6 | 13 | 21:43 | -22 | 21 |
| 20 | Kusatsu | 24 | 2 | 7 | 15 | 17:36 | -19 | 13 |
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