| Rank | Club | Pts | Game | W | D | L | GF | GA | GD | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Matsumoto Yamaga F.C. | 56 | 28 | 16 | 8 | 4 | 42 | 25 | 17 | |
| 2 | Oita Trinita | 50 | 28 | 15 | 5 | 8 | 50 | 35 | 15 | |
| 3 | FC Machida Zelvia | 50 | 27 | 14 | 8 | 5 | 47 | 34 | 13 | |
| 4 | Avispa Fukuoka | 46 | 26 | 13 | 7 | 6 | 37 | 26 | 11 | |
| 5 | Yokohama FC | 46 | 27 | 12 | 10 | 5 | 40 | 32 | 8 | |
| 6 | Tokyo Verdy | 45 | 28 | 12 | 9 | 7 | 39 | 29 | 10 | |
| 7 | Omiya Ardija | 44 | 28 | 13 | 5 | 10 | 45 | 33 | 12 | |
| 8 | Renofa Yamaguchi FC | 43 | 27 | 11 | 10 | 6 | 46 | 44 | 2 | |
| 9 | Montedio Yamagata | 40 | 27 | 11 | 7 | 9 | 33 | 30 | 3 | |
| 10 | Tokushima Vortis | 38 | 27 | 11 | 5 | 11 | 29 | 26 | 3 | |
| 11 | Fagiano Okayama | 38 | 27 | 10 | 8 | 9 | 28 | 26 | 2 | |
| 12 | Ventforet Kofu | 37 | 28 | 10 | 7 | 11 | 45 | 36 | 9 | |
| 13 | Mito Hollyhock | 36 | 28 | 10 | 6 | 12 | 33 | 32 | 1 | |
| 14 | Zweigen Kanazawa | 36 | 28 | 9 | 9 | 10 | 36 | 36 | 0 | |
| 15 | Tochigi SC | 35 | 28 | 9 | 8 | 11 | 28 | 33 | -5 | |
| 16 | JEF United Chiba | 35 | 28 | 10 | 5 | 13 | 49 | 55 | -6 | |
| 17 | FC Gifu | 32 | 28 | 9 | 5 | 14 | 36 | 41 | -5 | |
| 18 | Ehime FC | 30 | 28 | 8 | 6 | 14 | 23 | 38 | -15 | |
| 19 | Albirex Niigata | 29 | 28 | 8 | 5 | 15 | 29 | 43 | -14 | |
| 20 | Kamatamare Sanuki | 24 | 27 | 6 | 6 | 15 | 23 | 47 | -24 | |
| 21 | Roasso Kumamoto | 23 | 28 | 6 | 5 | 17 | 35 | 55 | -20 | |
| 22 | Kyoto Sanga F.C. | 22 | 27 | 6 | 4 | 17 | 23 | 40 | -17 |
