| Competition: | Japan Football League |
| Season: | 2003 |
| Dates: | 30 March – 23 November |
| Winners: | Otsuka Pharmaceuticals 1st JFL title 1st D3 title |
| Promoted: | none |
| Relegated: | Kyoto BAMB 1993 Jatco SC (folded) |
| League Topscorer: | Tatsuya Furuhashi (31 goal total) |
| Matches: | 240 |
| Total Goals: | 724 |
| Highest Attendance: | 4,123 (Round 18, SE Osaka vs. SE Tokyo) |
| Lowest Attendance: | 83 (Round 24, Kokushikan vs. Printing) |
| Average Attendance: | 573 |
| Prevseason: | 2002 |
| Nextseason: | 2004 |
The was the fifth 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 |  Tatsuya Furuhashi | Honda FC | |
| 2 | Yasuaki Oshima | Otsuka Pharmaceuticals | |
| 3 | Toshiro Tomochika | Ehime FC | |
Due to the Jatco team disbanding, the Regional League promotion series winner Thespa Kusatsu were promoted automatically. Runner-up Gunma Horikoshi were set to play Kyoto BAMB 1993 in the promotion and relegation series.
----
Gunma Horikoshi won the series at 8–2 aggregate score and earned promotion to JFL. Kyoto BAMB 1993 were relegated to Kansai regional league.