| Competition: | Japan Football League |
| Season: | 2006 |
| Dates: | 19 March – 3 December |
| Winners: | Honda FC 3rd JFL title 4th D3 title |
| Relegated: | Honda Lock |
| League Topscorer: | Tetsuya Okubo (26 goals total) |
| Matches: | 306 |
| Total Goals: | 945 |
| Highest Attendance: | 8,999 (Round 7, Rosso vs. Mizushima) |
| Lowest Attendance: | 78 (Round 24, SE Osaka vs. JEF Reserves |
| Average Attendance: | 986 |
| Prevseason: | 2005 |
| Nextseason: | 2007 |
The was the eighth season of the Japan Football League, the third tier of the Japanese football league system.
It was contested by 18 teams, and Honda FC won the championship.
Before the season two corporate clubs changed their names and were re-established as independent organizations. Denso SC became FC Kariya and FC Horikoshi became Arte Takasaki.
FC Ryukyu, JEF Reserves and Rosso Kumamoto were promoted from Regional leagues by the virtue of their placing in the Regional League promotion series, thus expanding the league to 18 teams.
At the J. League meeting in August, Rosso Kumamoto were approved as first J. League associate members, becoming eligible to J2 promotion. No such promotion took place because they failed to achieve at least 4th spot in the final standings.
| Rank | Scorer | Club | Goals[1] |
|---|---|---|---|
| 1 |  Tetsuya Okubo | Sagawa Express Tokyo | 26 |
| 2 | Yosuke Kobayashi | Yokogawa Musashino | 23 |
| Junya Nitta | Honda FC | 23 | |
| 4 | Yoshio Kitagawa | ALO's Hokuriku | 22 |
| 5 | Sho Gokyu | Sagawa Express Osaka | 21 |
| 6 | Hiroki Kishida | YKK AP | 20 |
| 7 | Kodai Suzuki | Honda FC | 18 |
| 8 | Hideki Uchiyama | SC Tottori | 17 |
| 9 | Yutaka Takahashi | Rosso Kumamoto | 15 |
| 10 | Kento Hori | Sagawa Express Tokyo | 14 |
Due to the merger of Sagawa Express teams into one club, the Regional League promotion series winners TDK SC were promoted automatically. FC Gifu were set to play Honda Lock in the promotion and relegation series.
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F.C. Gifu won the series at 8–1 aggregate score and earned promotion to JFL. Honda Lock were relegated to Kyushu regional league.