| Competition: | Japan Football League |
| Season: | 1999 |
| Dates: | 18 April – 7 November |
| Winners: | Yokohama FC 1st JFL title 1st D3 title |
| Promoted: | Mito HollyHock |
| League Topscorer: | Marcus (22 goals total) |
| Matches: | 108 |
| Total Goals: | 386 |
| Highest Attendance: | 11,283 (Round 2, Yokohama vs. Jatco) |
| Lowest Attendance: | 113 (Round 4, Kokushikan vs. Jatco) |
| Average Attendance: | 1,084 |
| Prevseason: | 1998 (former JFL) |
| Nextseason: | 2000 |
The was the first season of the Japan Football League, the third tier of the Japanese football league system.
After the dissolution of former Japan Football League in order to form J. League Division 2, the new Japan Football League was established from this season as the nationwide top division for amateur clubs. It was originally planned to have 8 clubs, including seven former JFL clubs and Yokogawa Electric, promoted from Kantō Soccer League, one of nine Japanese Regional Leagues. But it eventually became nine-club structure by accepting Yokohama FC, which was established by supporters of defunct Yokohama Flügels, as an associate member as an extralegal measures. Nine clubs played 24 matches each, in triple round-robin format. Yokohama F.C. won the championship but under the conditions of their associate membership were not eligible to promotion and had to stay in JFL for the next year.
| Rank | Scorer | Club | Goals |
|---|---|---|---|
| 1 |  Marcus | Honda Motors | 22 |
| 2 |  Kenji Arima | Yokohama FC | 19 |
| 3 | Mitsunori Yabuta | Yokohama FC | 12 |
| 4 | Hiroyasu Ibata | Honda Motors | 11 |
| Hiroaki Tajima | Honda Motors | 11 | |
No relegation has occurred because the league was expanding to 12 teams. At the end of the season, the winner and runner-up of the Regional League promotion series, ALO's Hokuriku and Tochigi SC were promoted automatically. In addition, FC Kyoken and Shizuoka Sangyo University were included by JFA and College FA recommendations.