| Competition: | Japan Football League |
| Season: | 2009 |
| Dates: | 15 March – 29 November |
| Winners: | Sagawa Shiga 2nd JFL title 2nd D3 title |
| Promoted: | New Wave Kitakyushu |
| Relegated: | FC Kariya Mitsubishi Motors Mizushima |
| League Topscorer: | Shogo Shiozawa (17 goals total) |
| Matches: | 306 |
| Total Goals: | 775 |
| Highest Attendance: | 9,856 (Round 1, New Wave vs. JEF Reserves) |
| Lowest Attendance: | 109 (Round 28, Printing vs. Arte) |
| Average Attendance: | 1,189 |
| Prevseason: | 2008 |
| Nextseason: | 2010 |
The was the eleventh season of the Japan Football League, the third tier of the Japanese football league system.
At the end of the 2008 season, three new clubs were promoted from the Japanese Regional Leagues by virtue of their final placing in the Regional League promotion series:
Machida Zelvia and V-Varen Nagasaki were approved as J. League associate members at the annual meeting in January.
Sagawa Shiga won their second championship title since 2007 season.
| Rank | Scorer | Club | Goals[1] |
|---|---|---|---|
| 1 |  Shogo Shiozawa | SP Kyoto | 17 |
| 2 | Shingo Kinoshita | MIO Biwako Kusatsu | 15 |
| Gen Nakamura | Sagawa Shiga | 15 | |
| 4 | Keiichi Kubota | Arte Takasaki | 11 |
| Junya Nitta | Honda FC | 11 | |
| Toshitaka Tsurumi | Gainare Tottori | 11 | |
| 7 | Ryota Arimitsu | V-Varen Nagasaki | 10 |
 Hamed Koné | Gainare Tottori | 10 | |
| Shoma Mizunaga | Honda Lock | 10 | |
| Tomoya Osawa | Sagawa Shiga | 10 | |
| Yuya Sano | New Wave Kitakyushu | 10 | |
| Tatsuya Sekino | Yokogawa Musashino | 10 | |
Due to Kitakyushu being promoted and Mitsubishi Mizushima being relegated, the Regional League promotion series winner and runner-up, Matsumoto Yamaga and Hitachi Tochigi Uva respectively, were promoted automatically. Third-placed team, Zweigen Kanazawa were set to play FC Kariya in the promotion and relegation series.
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Zweigen Kanazawa won the series at 2–1 aggregate score and earned promotion to JFL. F.C. Kariya relegated to Tōkai regional league.