| Rank | Club | Pts | Game | W | D | L | GF | GA | GD | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Kashiwa Reysol | 58 | 28 | 17 | 7 | 4 | 42 | 19 | 23 | |
| 2 | Kyoto Sanga F.C. | 51 | 28 | 14 | 9 | 5 | 43 | 29 | 14 | |
| 3 | Omiya Ardija | 49 | 27 | 13 | 10 | 4 | 38 | 22 | 16 | |
| 4 | Mito Hollyhock | 48 | 28 | 12 | 12 | 4 | 34 | 19 | 15 | |
| 5 | Montedio Yamagata | 46 | 27 | 13 | 7 | 7 | 32 | 21 | 11 | |
| 6 | Yokohama FC | 45 | 27 | 13 | 6 | 8 | 42 | 29 | 13 | |
| 7 | Ventforet Kofu | 43 | 28 | 12 | 7 | 9 | 41 | 28 | 13 | |
| 8 | Zweigen Kanazawa | 43 | 28 | 10 | 13 | 5 | 36 | 23 | 13 | |
| 9 | Fagiano Okayama | 40 | 27 | 11 | 7 | 9 | 31 | 35 | -4 | |
| 10 | Albirex Niigata | 37 | 27 | 10 | 7 | 10 | 44 | 35 | 9 | |
| 11 | Tokushima Vortis | 37 | 27 | 10 | 7 | 10 | 33 | 34 | -1 | |
| 12 | V･Varen Nagasaki | 37 | 28 | 11 | 4 | 13 | 38 | 40 | -2 | |
| 13 | Tokyo Verdy | 37 | 27 | 9 | 10 | 8 | 36 | 39 | -3 | |
| 14 | Renofa Yamaguchi FC | 33 | 28 | 9 | 6 | 13 | 41 | 46 | -5 | |
| 15 | Ehime FC | 32 | 27 | 9 | 5 | 13 | 29 | 33 | -4 | |
| 16 | FC Ryukyu | 31 | 27 | 8 | 7 | 12 | 37 | 48 | -11 | |
| 17 | JEF United Chiba | 30 | 27 | 7 | 9 | 11 | 33 | 41 | -8 | |
| 18 | Avispa Fukuoka | 27 | 27 | 7 | 6 | 14 | 27 | 42 | -15 | |
| 19 | FC Machida Zelvia | 27 | 28 | 6 | 9 | 13 | 25 | 45 | -20 | |
| 20 | Tochigi SC | 24 | 28 | 4 | 12 | 12 | 22 | 37 | -15 | |
| 21 | Kagoshima United FC | 24 | 26 | 7 | 3 | 16 | 28 | 44 | -16 | |
| 22 | FC Gifu | 20 | 27 | 5 | 5 | 17 | 25 | 48 | -23 |
