| Rank | Club | Pts | Game | W | D | L | GF | GA | GD | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Matsumoto Yamaga F.C. | 76 | 41 | 21 | 13 | 7 | 54 | 34 | 20 | |
| 2 | Oita Trinita | 75 | 41 | 23 | 6 | 12 | 75 | 50 | 25 | |
| 3 | FC Machida Zelvia | 75 | 41 | 21 | 12 | 8 | 61 | 43 | 18 | |
| 4 | Yokohama FC | 73 | 41 | 20 | 13 | 8 | 62 | 44 | 18 | |
| 5 | Tokyo Verdy | 70 | 41 | 19 | 13 | 9 | 55 | 40 | 15 | |
| 6 | Avispa Fukuoka | 69 | 41 | 19 | 12 | 10 | 58 | 42 | 16 | |
| 7 | Omiya Ardija | 68 | 41 | 20 | 8 | 13 | 64 | 48 | 16 | |
| 8 | Ventforet Kofu | 59 | 41 | 16 | 11 | 14 | 56 | 45 | 11 | |
| 9 | Renofa Yamaguchi FC | 58 | 41 | 15 | 13 | 13 | 61 | 64 | -3 | |
| 10 | Mito Hollyhock | 57 | 41 | 16 | 9 | 16 | 47 | 43 | 4 | |
| 11 | Tokushima Vortis | 55 | 41 | 16 | 7 | 18 | 48 | 42 | 6 | |
| 12 | Montedio Yamagata | 55 | 41 | 14 | 13 | 14 | 48 | 50 | -2 | |
| 13 | JEF United Chiba | 54 | 41 | 16 | 6 | 19 | 72 | 72 | 0 | |
| 14 | Fagiano Okayama | 53 | 41 | 14 | 11 | 16 | 39 | 42 | -3 | |
| 15 | Albirex Niigata | 53 | 41 | 15 | 8 | 18 | 48 | 54 | -6 | |
| 16 | Zweigen Kanazawa | 52 | 41 | 13 | 13 | 15 | 49 | 47 | 2 | |
| 17 | Tochigi SC | 49 | 41 | 13 | 10 | 18 | 38 | 48 | -10 | |
| 18 | Ehime FC | 48 | 41 | 12 | 12 | 17 | 34 | 49 | -15 | |
| 19 | FC Gifu | 41 | 41 | 11 | 8 | 22 | 44 | 62 | -18 | |
| 20 | Kyoto Sanga F.C. | 40 | 41 | 11 | 7 | 23 | 38 | 58 | -20 | |
| 21 | Roasso Kumamoto | 31 | 41 | 8 | 7 | 26 | 47 | 79 | -32 | |
| 22 | Kamatamare Sanuki | 31 | 41 | 7 | 10 | 24 | 28 | 70 | -42 |
