List of winners of J3 League and predecessors
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.
(former) Japan Football League Division 2 (1992–1993)
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 |
Japan Football League (JFL) (1999–2013)
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.†Not promoted to J2
For additional promoted teams, the number in parentheses indicates their position after the end of the season.
J3 League (2014–present)
In 2014, J. League launched a fully professional third division.† 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.
Total wins
Clubs in bold compete in J3 as of 2025 season. Clubs in italic no longer exist.Years in italic indicate seasons of amateur football.
| 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 City FC | 1 | 0 | 2025 | — |
| 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 |
| Vanraure Hachinohe | 0 | 1 | — | 2025 |