| Competition: | Japan Football League |
| Season: | 2004 |
| Dates: | 28 March – 5 December |
| Winners: | Otsuka Pharmaceuticals 2nd JFL title 2nd D3 title |
| Promoted: | Otsuka Pharmaceuticals Thespa Kusatsu |
| Relegated: | Kokushikan University (expelled by JFA) |
| League Topscorer: | Takehiro Hayashi (21 goal total) |
| Matches: | 239 |
| Total Goals: | 746 |
| Highest Attendance: | 13,743 (Round 27, Thespa vs. Otsuka) |
| Lowest Attendance: | 85 (Round 23, Kokushikan vs. Tottori) |
| Average Attendance: | 1,141 |
| Prevseason: | 2003 |
| Nextseason: | 2005 |
The was the sixth season of the Japan Football League, the third tier of the Japanese football league system.
It was contested by 16 teams, and Otsuka Pharmaceuticals won the championship.
| Rank | Scorer | Club | Goals[1] |
|---|---|---|---|
| 1 |  Takehiro Hayashi | Otsuka Pharmaceuticals | 21 |
| 2 | Yasuaki Oshima | Otsuka Pharmaceuticals | 20 |
| 3 | Koji Murayama | Yokogawa Musashino | 18 |
| Junya Nitta | Honda FC | 18 | |
| 5 | Mitsuru Hasegawa | YKK AP | 16 |
| Toshiro Tomochika | Ehime FC | 16 | |
| 7 | Tatsuya Furuhashi | Honda FC | 15 |
| 8 | Youichi Mori | Gunma Horikoshi | 14 |
| 9 | Yosuke Kobayashi | Yokogawa Musashino | 12 |
| Takeshi Ushibana | YKK AP | 12 | |
| Atsushi Yoshimoto | Thespa Kusatsu | 12 | |
Because of promotion of Otsuka Pharmaceuticals and Thespa Kusatsu and expulsion of Kokushikan University, no relegation has occurred. After the season, Honda Lock, Mitsubishi Motors Mizushima and Ryutsu Keizai University were promoted from Regional Leagues by the virtue of their placing in the Regional League promotion series.