| Rank | Club | Pts | Game | W | D | L | GF | GA | GD | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Kashiwa Reysol | 84 | 42 | 25 | 9 | 8 | 85 | 33 | 52 | |
| 2 | Yokohama FC | 79 | 42 | 23 | 10 | 9 | 66 | 40 | 26 | |
| 3 | Omiya Ardija | 75 | 42 | 20 | 15 | 7 | 62 | 40 | 22 | |
| 4 | Tokushima Vortis | 73 | 42 | 21 | 10 | 11 | 67 | 45 | 22 | |
| 5 | Ventforet Kofu | 71 | 42 | 20 | 11 | 11 | 64 | 40 | 24 | |
| 6 | Montedio Yamagata | 70 | 42 | 20 | 10 | 12 | 59 | 40 | 19 | |
| 7 | Mito Hollyhock | 70 | 42 | 19 | 13 | 10 | 56 | 37 | 19 | |
| 8 | Kyoto Sanga F.C. | 68 | 42 | 19 | 11 | 12 | 59 | 56 | 3 | |
| 9 | Fagiano Okayama | 65 | 42 | 18 | 11 | 13 | 49 | 47 | 2 | |
| 10 | Albirex Niigata | 62 | 42 | 17 | 11 | 14 | 71 | 52 | 19 | |
| 11 | Zweigen Kanazawa | 61 | 42 | 15 | 16 | 11 | 58 | 46 | 12 | |
| 12 | V･Varen Nagasaki | 56 | 42 | 17 | 5 | 20 | 57 | 61 | -4 | |
| 13 | Tokyo Verdy | 55 | 42 | 14 | 13 | 15 | 59 | 59 | 0 | |
| 14 | FC Ryukyu | 49 | 42 | 13 | 10 | 19 | 57 | 80 | -23 | |
| 15 | Renofa Yamaguchi FC | 47 | 42 | 13 | 8 | 21 | 54 | 70 | -16 | |
| 16 | Avispa Fukuoka | 44 | 42 | 12 | 8 | 22 | 39 | 62 | -23 | |
| 17 | JEF United Chiba | 43 | 42 | 10 | 13 | 19 | 46 | 64 | -18 | |
| 18 | FC Machida Zelvia | 43 | 42 | 9 | 16 | 17 | 36 | 59 | -23 | |
| 19 | Ehime FC | 42 | 42 | 12 | 6 | 24 | 46 | 62 | -16 | |
| 20 | Tochigi SC | 40 | 42 | 8 | 16 | 18 | 33 | 53 | -20 | |
| 21 | Kagoshima United FC | 40 | 42 | 11 | 7 | 24 | 41 | 73 | -32 | |
| 22 | FC Gifu | 30 | 42 | 7 | 9 | 26 | 33 | 78 | -45 |
