Il existe presque 200 compagnies de transport sur rail au Japon.
Japan Railway : entreprises issues des anciens Japanese National Railways)
- Central Japan Railway Company
- East Japan Railway Company
- Hokkaido Railway Company
- Kyushu Railway Company
- Shikoku Railway Company
- West Japan Railway Company
- Japan Freight Railway Company
Chemins de fer privés : les quinze grands
- Hankyu Railway
- Hanshin Electric Railway
- Keihan Electric Railway
- Keihin Kyuko Electric Railway
- Keio Electric Railway
- Keisei Electric Railway
- Kinki Nippon Railway (Kintetsu)
- Nagoya Railroad (Meitetsu)
- Nankai Electric Railway
- Nishi-Nihon Railway
- Odakyu Electric Railway
- Sagami Railway
- Seibu Railway
- Tobu Railway
- Tokyo Kyuko Electric Railway
Autres chemins de fer privés
- Eizan Electric Railway
- Kishu Railway
- Kobe Electric Railway
- Mizuma Railway
- Nose Electric Railway
- Ohmi Railway
- Sanyo Electric Railway
Chemins de fer secondaires
- Asa Kaigan Railway
- Chizu Express
- Hojo Railway
- Hokuetsu Express
- Ihara Railway
- Ise Railway
- Kita Kinki Tango Railway
- Kobe Rapid Railway
- Kurihara Den'en Railway
- Miki Railway
- Nishikigawa Railway
- Noto Railway
- Shigaraki Kougen Railway
- Tosa Kuroshio Railway
- Wakasa Railway
Métros
- Kobe Municipal Transportation Bureau (Métro municipal de K?be)
- Kyoto Municipal Transportation Bureau (Métro municipal de Ky?to)
- Nagoya City Transportation Bureau (Métro municipal de Nagoya)
- Métro de T?ky?
- Osaka Municipal Transportation Bureau (Métro municipal d’?saka)
- Tokyo Metropolitan Bureau of Transportation
Monorails
- Monorail d'Inuyama
- Monorail de Kitakyushu
- Maihama Resort Line
- Monorail d'Osaka
- Monorail de Tama Toshi
- Monorail de Tokyo
- Yui Rail
Tramways
- Sapporo
- Hakodate
- Tokyo
- Toyohashi
- Toyama
- Takaoka
- Gifu (fermé en 2005)
- Kyoto
- Osaka
- Okayama
- Hiroshima (le plus grand réseau de tram du Japon)
- Matsuyama
- Kochi
- Nagasaki
- Kumamoto
- Kagoshima
Il faut y ajouter quelques lignes interurbaines qui servent de tram à l'intérieur des villes
Nouveaux systèmes de transport urbain
- Aichi Rapid Transit
- Hiroshima Rapid Transit
- Kobe New Transit (Portliner, Rokkoliner)
- Nagoya Guideway Bus
- New Tram (Nanko Port Town Line)
- Osakako Transportation System (OTS)
- Saitama Shintoshi Transit
- Skyrail Service
- Tokadai New Transit
- Yokohama Shintoshi Transit
- Yurikamome