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A national third tier of Japanese league football was first established in 1992, as the second division of former Japan Football League, though it only lasted for two seasons. In 1999, following the establishment of J.League Division 2, a new Japan Football League was created, fulfilling the third tier until a fully professional J3 League was launched in 2014.
The old Japan Football League was established simultaneously with creation of J.League and was initially a two-level tournament but that lasted only for two inaugural seasons.
| Season | Champions | Runners-up |
|---|---|---|
| 1992 | Chuo Bohan | Kyoto Shiko |
| 1993 | Honda Motors | PJM Futures |
With the establishment of J.League Division 2, the new Japan Football League was automatically moved a tier down the pyramid comparing to its discontinued namesake.
| Season | Champions | Runners-up | (Also) promoted |
|---|---|---|---|
| 1999 | Yokohama FC † | Honda Motors † | Mito HollyHock (3rd) |
| 2000 | Yokohama FC (2) | Honda Motors † | |
| 2001 | Honda Motors (2)† | Otsuka Pharmaceutical † | |
| 2002 | Honda Motors (3)† | Sagawa Express Tokyo † | |
| 2003 | Otsuka Pharmaceutical † | Honda FC † | |
| 2004 | Otsuka Pharmaceutical (2) | Honda FC † | Thespa Kusatsu (3rd) |
| 2005 | Ehime FC | YKK AP † | |
| 2006 | Honda FC (4)† | Sagawa Express Tokyo † | |
| 2007 | Sagawa Express † | Rosso Kumamoto | FC Gifu (3rd) |
| 2008 | Honda FC (5)† | Tochigi SC | Kataller Toyama (3rd) Fagiano Okayama (4th) |
| 2009 | Sagawa Shiga (2)† | Yokogawa Musashino † | New Wave Kitakyushu (4th) |
| 2010 | Gainare Tottori | Sagawa Shiga † | |
| 2011 | Sagawa Shiga (3)† | Nagano Parceiro † | Machida Zelvia (3rd) Matsumoto Yamaga (4th) |
| 2012 | V-Varen Nagasaki | Nagano Parceiro † | |
| 2013 | Nagano Parceiro † | Kamatamare Sanuki | |
†Not promoted to J2
For additional promoted teams, the number in parentheses indicates their position after the end of the season.
In 2014, J. League launched a fully professional third division.
| Season | Champions | Runners-up | Playoff Winners |
|---|---|---|---|
| 2014 | Zweigen Kanazawa | Nagano Parceiro ‡ | |
| 2015 | Renofa Yamaguchi | Machida Zelvia | |
| 2016 | Oita Trinita | Tochigi SC ‡ | |
| 2017 | Blaublitz Akita † | Tochigi SC | |
| 2018 | FC Ryukyu | Kagoshima United | |
| 2019 | Giravanz Kitakyushu | Thespakusatsu Gunma | |
| 2020 | Blaublitz Akita (2) | SC Sagamihara | |
| 2021 | Roasso Kumamoto | Iwate Grulla Morioka | |
| 2022 | Iwaki FC | Fujieda MYFC | |
| 2023 | Ehime FC (2) | Kagoshima United | |
| 2024 | Omiya Ardija | FC Imabari | Kataller Toyama (3rd) |
† Not promoted to J2.
‡ Not promoted to J2 due to a loss in the Promotion/Relegation series.
For play-off winners, the number in parentheses indicates their position after the end of the season.
Clubs in bold compete in J3 as of 2025 season. Clubs in italic no longer exist.
Years in italic indicate seasons of amateur football (former and new Japan Football League).
| Club | Winners | Runners-up | Winning seasons | Runners-up seasons |
|---|---|---|---|---|
| Honda FC | 5 | 4 | 1993, 2001, 2002, 2006, 2008 | 1999, 2000, 2003, 2004 |
| Sagawa Shiga | 3 | 1 | 2007, 2009, 2011 | 2010 |
| Tokushima Vortis | 2 | 1 | 2003, 2004 | 2001 |
| Yokohama FC | 2 | 0 | 1999, 2000 | — |
| Ehime FC | 2 | 0 | 2005, 2023 | — |
| Blaublitz Akita | 2 | 0 | 2017, 2020 | — |
| Nagano Parceiro | 1 | 3 | 2013 | 2011, 2012, 2014 |
| Roasso Kumamoto | 1 | 1 | 2021 | 2007 |
| Avispa Fukuoka | 1 | 0 | 1992 | — |
| Gainare Tottori | 1 | 0 | 2010 | — |
| V-Varen Nagasaki | 1 | 0 | 2012 | — |
| Zweigen Kanazawa | 1 | 0 | 2014 | — |
| Renofa Yamaguchi | 1 | 0 | 2015 | — |
| Oita Trinita | 1 | 0 | 2016 | — |
| FC Ryukyu | 1 | 0 | 2018 | — |
| Giravanz Kitakyushu | 1 | 0 | 2019 | — |
| Iwaki FC | 1 | 0 | 2022 | — |
| Omiya Ardija | 1 | 0 | 2024 | — |
| Tochigi SC | 0 | 3 | — | 2008, 2016, 2017 |
| Sagawa Express Tokyo | 0 | 2 | — | 2002, 2006 |
| Kagoshima United | 0 | 2 | — | 2018, 2023 |
| Kyoto Sanga | 0 | 1 | — | 1992 |
| Tosu Futures | 0 | 1 | — | 1993 |
| YKK AP | 0 | 1 | — | 2005 |
| Yokogawa Musashino | 0 | 1 | — | 2009 |
| Kamatamare Sanuki | 0 | 1 | — | 2013 |
| Machida Zelvia | 0 | 1 | — | 2015 |
| Thespa Gunma | 0 | 1 | — | 2019 |
| SC Sagamihara | 0 | 1 | — | 2020 |
| Iwate Grulla Morioka | 0 | 1 | — | 2021 |
| Fujieda MyFC | 0 | 1 | — | 2022 |
| FC Imabari | 0 | 1 | — | 2024 |
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| Leagues (2025) |
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| Cups (2025) |
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