| Competition: | Japan Football League |
| Season: | 1996 |
| Winners: | Honda |
| Promoted: | Vissel Kobe |
| Relegated: | Tosu Futures folded Cosmo Oil Yokkaichi folded |
| Matches: | 240 |
| Total Goals: | 825 |
| Prevseason: | 1995 |
| Nextseason: | 1997 |
Statistics of Japan Football League in the 1996 season.
It was contested by 16 teams, and Honda won the championship. However, citing continuing corporate ownership, they were refused promotion by the J.League, who took in the runner-up, Vissel Kobe, instead.
Newly promoted before the season were Nippon Denso, later known as FC Kariya, and Oita Trinity, later known as Oita Trinita.
| Pos | Club | P | W | L | F | A | GD | Pts | Notes |
| 1 | Honda | 30 | 25 | 5 | 83 | 35 | 48 | 75 | Champions (Refused promotion) |
| 2 | Vissel Kobe | 30 | 25 | 5 | 78 | 32 | 46 | 75 | Promoted to J.League |
| 3 | Tokyo Gas | 30 | 24 | 6 | 63 | 28 | 35 | 73 | |
| 4 | Tosu Futures | 30 | 20 | 10 | 68 | 43 | 25 | 62 | Folded |
| 5 | Consadole Sapporo | 30 | 20 | 10 | 60 | 43 | 17 | 62 | |
| 6 | Brummell Sendai | 30 | 18 | 12 | 67 | 52 | 15 | 56 | |
| 7 | Otsuka Pharmaceutical | 30 | 18 | 12 | 56 | 41 | 15 | 55 | |
| 8 | Montedio Yamagata | 30 | 16 | 14 | 45 | 49 | -4 | 49 | |
| 9 | Fujitsu Kawasaki | 30 | 15 | 15 | 48 | 45 | 3 | 45 | |
| 10 | Oita Trinity | 30 | 13 | 17 | 42 | 52 | -10 | 39 | |
| 11 | Ventforet Kofu | 30 | 11 | 19 | 50 | 56 | -6 | 33 | |
| 12 | Cosmo Oil Yokkaichi | 30 | 11 | 19 | 31 | 49 | -28 | 33 | Folded |
| 13 | NTT Kanto | 30 | 7 | 23 | 36 | 55 | -19 | 23 | |
| 14 | Fukushima | 30 | 7 | 23 | 30 | 63 | -33 | 22 | |
| 15 | Denso | 30 | 5 | 25 | 40 | 90 | -50 | 16 | |
| 16 | Seino Transportation | 30 | 5 | 25 | 28 | 82 | -54 | 15 |