
Arte Takasaki was a Japanese football club based in Takasaki, Gunma Prefecture, formerly of the Japan Football League. Their team colours were black and red.

Azul Claro Numazu is a Japanese professional football team based in Numazu, Shizuoka Prefecture. They earned promotion to play at the nationwide third-tier J3 League starting in 2017.

Blaublitz Akita is a Japanese professional association football team based in Akita, Akita Prefecture. In 2014 they entered the J3 League after previously playing in the Japan Football League, the third tier of the Japanese association football league system. Due to the club's former ownership by TDK, most of players were the employees of TDK's Akita factory. The club currently plays in the J2 League, which is the second tier of football in the country. Their home stadium is Soyu Stadium, also known as "Yabase". The club practices at the adjacent Akigin Stadium and Space Project Dream Field.

Briobecca Urayasu are a Japanese football (soccer) club based in Urayasu, Chiba. They play in the Kantō Soccer League.

Cobaltore Onagawa is a football (soccer) club based in Onagawa, the main and only city forming the Oshika District, which is located in Miyagi Prefecture in Japan. They play in the Tohoku Soccer League, which is part of Japanese Regional Leagues. The name Cobaltore comes from the combination of two Spanish words: cobalto, referring to cobalt blue, and floresta, meaning "forest".

Ehime Football Club (愛媛フットボールクラブ) is a professional football club based in Matsuyama, the capital city of Ehime Prefecture of Japan. After winning the JFL championship in 2005, the club now plays in J2 League.

Fagiano Okayama is a Japanese football club based in Okayama, the capital of Okayama Prefecture. They play in the J2 League, the second tier of the country's football league system. Their home stadium is City Light Stadium, in Okayama City, though some home matches are played at Tsuyama Stadium, in Tsuyama.

FC Imabari (FC今治) is a Japanese football club based in Imabari, Ehime Prefecture. They play in the J3 League.

FC Kariya are a Japanese football club based in Kariya, Aichi. They played in the first division of Tōkai Adult Soccer League and they're aiming towards professional leagues. In 2021 season, they currently play in the Japan Football League.

Football Club Machida Zelvia is a Japanese football club based in Machida, Tokyo.

Maruyasu Industries FC , playing as FC Maruyasu Okazaki , is a Japanese professional football team based in Okazaki, Aichi Prefecture. They currently play in Japan Football League, the fourth tier of Japanese nationwide football system.

FC Osaka is a Japanese football club playing in the Japan Football League, the fourth tier in the Japanese football league system. The top team name FC Osaka was changed to F.C. Osaka as of January 1, 2021. On January 12, 2022, the name was changed again to FC Osaka.

FC Ryukyu are an Association football club from the Okinawa Prefecture, Japan. They currently play in Japan's J2 League.

Fujieda MYFC are a Japanese J3 League football club based in Fujieda, Shizuoka. It is funded by online subscribers and is the first of its kind in Japan.

Fukushima United FC is a Japanese football club from Fukushima City, the capital of Fukushima Prefecture.

SC Gainare Tottori are a Japanese football club, based in Tottori, Tottori. They play in the J3 League. Their team colour is green.

Football Club Gifu, abbreviated as F.C. Gifu is a Japanese football club based in Gifu, Japan. They play in the J3 League, the third tier of Japanese professional football. They also run a reserve team that play in the Tōkai Adult League Division 1.

Giravanz Kitakyushu is a Japanese football club based in Kitakyushu, Fukuoka Prefecture. The club's name was changed from New Wave Kitakyushu as of 1 December 2009. They played in the Japan Football League from 2008–2009, and were promoted to J. League Division 2 (J2) for the 2010 season. They played in J2 until the 2016 season, but suffered relegation to the 2017 J3 League after being ranked 22nd. After slumping to the bottom of the 2018 J3 League, they bounced back to become champions in 2019, so were then promoted back to J2 for the 2020 season.

Honda FC is a Japanese professional football club based in Hamamatsu, Shizuoka. They play in the Japan Football League.

Honda Lock SC are a Japanese football (soccer) club based in Miyazaki, the capital city of Miyazaki Prefecture. They play in the Japan Football League. Their team colour is red.

Iwaki FC is a football (soccer) club based in Iwaki, a city in Fukushima Prefecture, Japan. The club currently play in J3 League, which is the 3rd level in the Japanese football pyramid.

Kagoshima United FC is a football club in Japan that was formed from the merger of Volca Kagoshima and FC Kagoshima, both have been playing in Kyushu Soccer League before the merger. Their top team currently plays in J3 League, and their secondary team plays in Kyushu Soccer League.

Kamatamare Sanuki is a football club based in Takamatsu, the capital city of Kagawa Prefecture of Japan. They currently play in the J3 League. They entered the J League in 2014 after finishing as runner-up in the Japan Football League in 2013. The first part of their name was coined by combining the Japanese word Kamatama and the Italian Mare ("Sea"). The second part is what Kagawa Prefecture used to be called. Their name as well as their crest, which also features a kamatama udon bowl, are so unique that the club instantly became one of the best-known non-J. League sides in Japan when announced in October 2005.

Kataller Toyama is a football club in Japan that was formed from the merger of the ALO's Hokuriku and YKK AP SC. The club currently plays in J3 League.

Kōchi United Sports Club, is a football club based in Kōchi, the capital city of Kōchi Prefecture in Japan. They played in the Shikoku Soccer League, one of the Japanese Regional Leagues from 2016–2019, winning it three times in a row from 2017–19. In 2019 they finished 2nd in the Japanese Regional Football League Competition, earning promotion to the Japan Football League from the 2020 season. In November 2021 they applied for J.League 100 Year Plan club status with the aim of becoming a fully professional club in the future.

Matsue City FC is a professional football club based in Matsue, which is located in Shimane Prefecture in Japan. They play in the Japan Football League. The team's name will be changed to FC Kagura Shimane on February 1, 2022.

Matsumoto Yamaga Football Club is the Japanese football (soccer) club based in Matsumoto, Nagano Prefecture. The club currently play in the J3 League. It was previously promoted to the J1 League in 2015 and 2019 and relegated to the J3 League in 2021, but was each time relegated after one season in the first tier of Japanese football until relegated after two season in the second tier of Japanese football.

MIO Biwako Shiga is a Japanese football club based in Kusatsu, Shiga Prefecture, although they also play matches in Ōtsu and Konan.

Mito HollyHock is a Japanese professional football (soccer) club, currently playing in the J2 League. The team's hometown is located in Mito, Ibaraki Prefecture.

Mitsubishi Mizushima F.C. are a Japanese football club based in Kurashiki, Okayama. They play in the Chūgoku Soccer League.

AC Nagano Parceiro (AC長野パルセイロ) is a Japanese football club based in Nagano. They play in J3 League. The club name parceiro means "partner" in Portuguese.

Nara Club is a Japanese football (soccer) club based in Nara, Nara Prefecture. They play in Japan Football League.

ReinMeer Aomori is a Japanese football club based in Aomori, the capital city of Aomori Prefecture. They play in the Japan Football League. Their team colour is blue.

Renofa Yamaguchi FC is a Japanese professional football club based in Yamaguchi, the capital of Yamaguchi Prefecture. They play in the J2 League, the second tier of the country's football league system.

Roasso Kumamoto is a Japanese football club based in Kumamoto, the capital city of Kumamoto Prefecture. The club currently plays in the J3 League, which is the third tier of football in the country. Roasso is a portmanteau of the Italian words rosso and asso, meaning "red ace".

Ryutsu Keizai University FC are a Japanese football (soccer) club based in Ryugasaki, Ibaraki Prefecture. They play in Division 1 of Kantō Soccer League. Their team colours are grey and navy.

Sagawa Shiga Football Club , formerly Sagawa Express Soccer Club , was an amateur Japanese football club based in Moriyama, Shiga. They were members of the Japan Football League (JFL). The club formed in 2007 from a merger of two Sagawa Express corporation football clubs in JFL; Sagawa Express Tokyo S.C. and Sagawa Express Osaka S.C.. The Tokyo side had been in JFL since 2001 and the Osaka side since 2002. The announcement of the merger was on September 14, 2006 and its base would be moved to Shiga prefecture, the company's corporate base. Blue and silver were their team colours. Their home stadium was the Sagawa Express Moriyama Stadium in Moriyama, Shiga.

SC Sagamihara is a Japanese association football club based in Sagamihara, Kanagawa Prefecture.

Sony Sendai FC is a Japanese football club based in Sendai, Miyagi Prefecture, Japan that plays in the Japan Football League. The team colour is navy.

SP Kyoto FC was a Japanese football club based in Muko, Kyoto, Japan. They played for the last time in Japan Football League for 2015 season.

Suzuka Point Getters is a Japanese professional football club based in Suzuka, Mie Prefecture. They play in Japan Football League.

Tegevajaro Miyazaki is a Japanese football club based in Miyazaki, the capital city of Miyazaki Prefecture. They play in the J3 League.

Thespakusatsu Gunma is a professional football (soccer) club based in Maebashi, Gunma Prefecture in Japan. The club plays in the J2 League, the second division of professional football in Japan.

Tochigi City Football Club (栃木シティフットボールクラブ) is a Japanese football club based in Tochigi Prefecture.

Tochigi Soccer Club (栃木サッカークラブ), commonly referred to as Tochigi SC are a football club based in Utsunomiya, Tochigi Prefecture, Japan. They will play in the J2 League. The team's colour is yellow.

Tokushima Vortis is a Japanese professional football club, currently playing in the J2 League. The team is located in Tokushima, Tokushima Prefecture. Their home stadium is Naruto Otsuka Sports Park Pocari Sweat Stadium, in Naruto, Tokushima.

Tokyo Musashino United F.C. is a football club based in Musashino, Tokyo, Japan. They play in the Japan Football League. Their team colour is blue.

V-Varen Nagasaki is a Japanese J2 League football club based in Nagasaki. The club was established in 1985 as Ariake SC till they merged with Kunimi FC in 2004 and adopted the present name in 2005.

Vanraure Hachinohe is a football club based in Hachinohe, a city in the southeastern part of Aomori Prefecture in Japan. They currently play in the J3 League. The name Vanraure comes from the combination of two Italian words: derivante, meaning "origin"; and australe, meaning "southern". It thus refers to the origin of the club in the southern area of Hachinohe, in the former village of Nangō.

Veertien Mie (ヴィアティン三重) is a Japanese football club based between Kuwana and Yokkaichi, Mie Prefecture. They play in the Japan Football League.

Verspah Oita is a Japanese football club currently competing in the Japan Football League. The year 2012 is their first year in the JFL after they were promoted from the 2011 Kyushu Soccer League.

YKK AP S.C. is a Japanese football club based in Kurobe, Toyama Prefecture. They play in Toyama Prefectural League. Their team colour is blue.

Yokohama FC is a Japanese professional football club based in Yokohama, Kanagawa Prefecture, part of the Greater Tokyo Area. The club currently plays in the J2 League, which is the second tier of football in the country. The club was formed by fans of Yokohama Flügels as a protest against Flügels' merger with Yokohama Marinos in 1999, becoming the first supporter-owned professional sports team in Japan.

Yokohama Sports & Culture Club , commonly referred to as simply Y.S.C.C. or Y.S.C.C. Yokohama is a Japanese multisports club based in Yokohama. Although they compete in a number of different sports, YSCC is best known for its association football team that currently plays in J3 League.

Zweigen Kanazawa is a Japanese football club based in Kanazawa, Ishikawa Prefecture. They play in the J2 League.