| Pos | Team | PL | GD | PTS |
|---|---|---|---|---|
| Japan Football League 2025 | ||||
| 1 |  Honda | 30 | +23 | 60 |
| 2 |  Biwako Shiga | 30 | +12 | 56 |
| 3 |  Urayasu | 30 | +10 | 52 |
| 4 |  TIAMO Hirakata | 30 | +16 | 50 |
| 5 |  Reinmeer Aomori | 30 | +7 | 50 |
| 6 |  Verspah Oita | 30 | +8 | 49 |
| 7 |  Veertien Mie | 30 | +13 | 45 |
| 8 |  Okinawa SV | 30 | -2 | 43 |
| 9 |  Grulla Morioka | 30 | -4 | 39 |
| 10 |  Honda Lock | 30 | -1 | 34 |
| 11 |  Maruyasu Okazaki | 30 | -9 | 34 |
| 12 |  Criacao Shinjuku | 30 | -5 | 33 |
| 13 |  YSCC | 30 | -21 | 30 |
| 14 |  Tokyo Musashino City | 30 | -20 | 29 |
| 15 |  Suzuka Unlimited | 30 | -16 | 28 |
| 16 |  Porvenir Asuka | 30 | -11 | 24 |