| Rank | Club | Pts | Game | W | D | L | GF | GA | GD | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Matsumoto Yamaga F.C. | 69 | 37 | 19 | 12 | 6 | 52 | 33 | 19 | |
| 2 | Oita Trinita | 66 | 37 | 20 | 6 | 11 | 67 | 44 | 23 | |
| 3 | FC Machida Zelvia | 65 | 35 | 18 | 11 | 6 | 55 | 38 | 17 | |
| 4 | Avispa Fukuoka | 64 | 37 | 18 | 10 | 9 | 52 | 36 | 16 | |
| 5 | Omiya Ardija | 63 | 37 | 19 | 6 | 12 | 59 | 43 | 16 | |
| 6 | Yokohama FC | 63 | 37 | 17 | 12 | 8 | 55 | 41 | 14 | |
| 7 | Tokyo Verdy | 63 | 37 | 17 | 12 | 8 | 50 | 36 | 14 | |
| 8 | Tokushima Vortis | 54 | 37 | 16 | 6 | 15 | 47 | 37 | 10 | |
| 9 | Ventforet Kofu | 52 | 37 | 14 | 10 | 13 | 52 | 41 | 11 | |
| 10 | Montedio Yamagata | 51 | 37 | 13 | 12 | 12 | 44 | 45 | -1 | |
| 11 | Renofa Yamaguchi FC | 51 | 36 | 13 | 12 | 11 | 59 | 62 | -3 | |
| 12 | Zweigen Kanazawa | 49 | 37 | 13 | 10 | 14 | 45 | 42 | 3 | |
| 13 | Fagiano Okayama | 49 | 37 | 13 | 10 | 14 | 37 | 39 | -2 | |
| 14 | JEF United Chiba | 48 | 37 | 14 | 6 | 17 | 65 | 66 | -1 | |
| 15 | Mito Hollyhock | 47 | 37 | 13 | 8 | 16 | 40 | 40 | 0 | |
| 16 | Albirex Niigata | 46 | 37 | 13 | 7 | 17 | 42 | 51 | -9 | |
| 17 | Tochigi SC | 45 | 37 | 12 | 9 | 16 | 34 | 43 | -9 | |
| 18 | Ehime FC | 43 | 37 | 11 | 10 | 16 | 31 | 45 | -14 | |
| 19 | Kyoto Sanga F.C. | 37 | 37 | 10 | 7 | 20 | 36 | 51 | -15 | |
| 20 | FC Gifu | 36 | 37 | 10 | 6 | 21 | 41 | 60 | -19 | |
| 21 | Kamatamare Sanuki | 29 | 36 | 7 | 8 | 21 | 26 | 65 | -39 | |
| 22 | Roasso Kumamoto | 27 | 37 | 7 | 6 | 24 | 42 | 73 | -31 |
