Here is a list of MMA gyms in the Tokyo Metropolitan area.
AKZA in Niiza, 3 minutes from Niiza Station on the JR Musashino Line
Alliance Square (Tsuyoshi Kosaka, TK’s gym) in Akasaka/near Roppongi- Tokyo Metro (Subway) Chiyoda Line, Nogizaka Station
Brave (Kazuyuki Miyata’s gym, 2 locations) in Kita-Senju, Tokyo – JR Joban Line, Chiyoda Line, Tobu Isesaki Line, Tsukuba Express, Kita-Senju Station, and Misato, Saitama – JR Musashino Line, Misato or Shin-Misato Stations.
Brightness Monma Dojo (Hidetaka Monma’s gym) in Adachi-ward – Tobu Isesaki Line, Nishi-Arai Station
Deep Impact Gym in Okubo – JR
Grabaka (2 locations)
Hearts (Kenji Osawa, formerly of Wajutsu Keishukai) – JR Shinjuku Station (south exit), Toei Shinjuku Line (Shinjuku Station), Odakyu Line (South Shinjuku Station)
Krazy Bee (Yamamoto “Kid’s” gym) in Magome – Toei Asakusa Line, Magome Station
Mach Dojo in Sugamo, JR Yamanote Line, Sugamo Station
Paraestra (mainly jiu-jitsu with some Shooto classes)
- Edogawa-ku – (Subway) Tozai Line, Nishi-Kasai Station
- Edogawa-ku – JR Sobu Line, Koiwa Station
- Nerima-ku – Toei Oedo Line, Shin-Egota Station
- 3 locations in Chiba
Purebred (Shooto) in Saitama, JR Utsunomiya Line, Higashi-Omiya Station
Shooting Gym (Shooto) in Yokohama, JR (and other) lines, Yokohama Station
RSCL Gym (Takanori Gomi’s gym) in Suginami-ward, Keio Inokashira Line, Kugayama Station
Roots Gym (Rumina Sato’s gym) in Odawara, JR, Odawara Station
Toikatsu Dojo in Nakano, JR Chuo Line, Nakano Station; (Subway) Tozai Line – Nakano Station, Marunouchi Line – Shin-Nakano Station, Seibu Ikebukuro Line – Araiyakushi-mae Station
Tribe Tokyo MMA in Nerima, 7-minute walk from Nerima station.
U-File (5 locations)
- WK main gym: (Subway) Marunouchi Line/Chiyoda Line, Shin-Ochanomizu Station and JR Sobu Line, Ochanomizu Station
- WK RJW: (Subway) Tozai Line, Monzen-Nakacho Station
Yoshida Dojo (5 locations)
Note that most of these gyms do not offer information or instruction in English, but I have not found this a problem. Rather than trying to contact them, it is often best to visit the gym in the evening and speak to someone there. Someone with some, or at least limited English ability should be able to help you.