| Line | Railway | Km | Linetype |
| A | Top | ||
| Aboshi | Sanyō Dentetsu | 8.5 | Non JR railway |
| Abukuma kyūkō (Abukuma express) | Abukyū | 54.9 | Non JR railway |
| Agatsuma | JR East | 55.6 | JR railway |
| Aichi kanjō (Aichi Loop) | Aikan | 45.3 | Non JR railway |
| Aizu | Aizu Tetsudō | 57.4 | Non JR railway |
| Aizu-Kinugawa | Yagan | 30.7 | Non JR railway |
| Akabane | JR East | 5.5 | JR railway |
| Akasako | Nagasaki | 0.4 | Tramway |
| Akechi | Aketetsu | 25.1 | Non JR railway |
| Akita Nairiku | Akita Nairiku | 94.2 | Non JR railway |
| Akita Shinkansen | JR East | Shinkansen | |
| Akō | JR West | 57.4 | JR railway |
| Amagi | Nishitetsu | 17.9 | Non JR railway |
| Amagi | Amagi | 13.7 | Non JR railway |
| Ao | Shintetsu | 29.2 | Non JR railway |
| Aoimori Tetsudō | Aoimori | 121.9 | Non JR railway |
| Aonami | Nagoya Rinkai | Non JR railway (Nickname) | |
| Arashiyama | Hankyū | 4.1 | Non JR railway |
| Arashiyama Hon (Randen) | Keifuku | 7.2 | Non JR railway |
| Arida * | Arida | 5.6 | Non JR railway |
| Arima | Shintetsu | 22.5 | Non JR railway |
| Asa (Gomen-Nahari) | Tosa Kuroshio | 42.7 | Non JR railway |
| Asakusa | TOEI | 18.3 | Metro (Subway) |
| Asanogawa | Hokutetsu | 6.8 | Non JR railway |
| Asatō | Asatetsu | 8.5 | Non JR railway |
| Astram (Hiroshima-Shinkōtsu-Ichigō [1-gō]) | Hiroshima Kōsoku | 18.4 | New transit system |
| Aterazawa | JR East | 24.3 | JR railway |
| Atsumi | Toyotetsu | 18.0 | Non JR railway |
| Azumada Hon (branch) | Toyotetsu | 0.6 | Tramway |
| Azumada Hon (Shinai) | Toyotetsu | 4.8 | Tramway |
| B | Top | ||
| Banetsu-sai | JR East | 175.6 | JR railway |
| Banetsu-tō | JR East | 85.6 | JR railway |
| Bantan | JR West | 65.7 | JR railway |
| Bessho | Ueda | 11.6 | Non JR railway |
| Bisai | Meitetsu | 30.9 | Non JR railway |
| Biwako | JR West | JR railway (Nickname) | |
| Blue - Line 1 | Yokohama Subway | 19.7 | Metro (Subway) |
| Blue - Line 3 | Yokohama Subway | 20.7 | Metro (Subway) |
| C | Top | ||
| Chiba | Keisei | 12.9 | Non JR railway |
| Chichibu | Seibu | 19.0 | Non JR railway |
| Chichibu Hon | Chichibu | 71.7 | Non JR railway |
| Chihara | Keisei | 10.9 | Non JR railway |
| Chikkō | Meitetsu | 1.5 | Non JR railway |
| Chikuhi (Meinohama - Karatsu) | JR Kyūshū | 42.6 | JR railway |
| Chikuhi (Yamamoto - Imari) | JR Kyūshū | 25.7 | JR railway |
| Chikuhō Denki Tetsudō | Chikuhō Denki | 16.0 | Non JR railway |
| Chikuhō Hon | JR Kyūshū | 66.1 | JR railway |
| Chita Shin | Meitetsu | 13.9 | Non JR railway |
| Chitose | JR Hokkaidō | 56.6 | JR railway |
| Chitose (Airport branch) | JR Hokkaidō | 2.6 | JR railway |
| Chiyoda | Tōkyō Metro | 21.9 | Metro (Subway) |
| Chiyoda (Kita-Ayase branch) | Tōkyō Metro | 2.1 | Metro (Subway) |
| Chizu | Chizukyū | 56.1 | Non JR railway |
| Chōkaisanroku | Yuri Kōgen | 23.0 | Non JR railway |
| Chōshi Denki Tetsudō | Chōshi | 6.4 | Non JR railway |
| Chūō | Ōsaka-shi | 17.9 | Metro (Subway) |
| Chūō - Sōbu kankō | JR East | 60.2 | JR railway (Virtual line) |
| Chūō Hon (East) | JR East | 220.8 | JR railway |
| Chūō Hon (Tatsuno branch) | JR East | 27.7 | JR railway |
| Chūō Hon (West) | JR Central | 174.8 | JR railway |
| D | Top | ||
| Dai-ikki (No 1) | Kagoshima-shi | 3.0 | Tramway |
| Dai-niki (No 2) | Kagoshima-shi | 1.0 | Tramway |
| Daishi | Keikyū | 4.5 | Non JR railway |
| Daishi | Tōbu | 1.0 | Non JR railway |
| Daiyūzan | Izu Hakone | 9.6 | Non JR railway |
| Dazaifu | Nishitetsu | 2.4 | Non JR railway |
| Den'en-toshi | Tōkyū | 31.5 | Non JR railway |
| Disney Resort | Maihama Resort | 5.0 | Monorail |
| Dōbutsuen | Keiō | 2.0 | Non JR railway |
| Dōmyōji | Kintetsu | 2.2 | Non JR railway |
| Dosan | JR Shikoku | 198.7 | JR railway |
| E | Top | ||
| Eba | Hiroden | 2.6 | Tramway |
| Echigo | JR East | 83.8 | JR railway |
| Eiheiji | Echizen | 6.2 | Non JR railway |
| Eizan Hon | Eiden | 5.6 | Non JR railway |
| Enoshima | Shōnan Monorail | 6.6 | Monorail |
| Enoshima | Odakyū | 27.6 | Non JR railway |
| Enoshima dentetsu | Enoden | 10.0 | Non JR railway |
| Enshū Tetsudō | Enshū | 17.8 | Non JR railway |
| Esashi | JR Hokkaidō | 79.9 | JR railway |
| Etsumi-hoku (Kuzuryū) | JR West | 52.5 | JR railway |
| Etsumi-nan | Nagatetsu | 72.1 | Non JR railway |
| F | Top | ||
| Flower (Furawa) Nagai | Yamagata | 30.5 | Non JR railway |
| Fuji kyūkō | Fujikyū | Non JR railway (Nickname) | |
| Fujikoshi | Chitetsu | 3.3 | Non JR railway |
| Fujisaki | Kumaden | 2.3 | Non JR railway |
| Fukubu | Fukutetsu | 20.9 | Non JR railway |
| Fukubu (branch) | Fukutetsu | 0.5 | Tramway |
| Fukuchiyama | JR West | 106.5 | JR railway |
| Fukuen | JR West | 78.0 | JR railway |
| Fukutoshin | Tōkyō Metro | 20.2 | Metro (Subway) |
| Furano | JR Hokkaidō | 54.8 | JR railway |
| Furusato-Ginga | Hokkaidō Chihoku Kōgen | 140.0 | Non JR railway |
| G | Top | ||
| Gakkentoshi | JR West | JR railway (Nickname) | |
| Gakuentoshi | JR Hokkaidō | JR railway (Nickname) | |
| Gakunan Tetsudō | Gakunan | 9.2 | Non JR railway |
| Gamagōri | Meitetsu | 17.6 | Non JR railway |
| Gantoku | JR West | 43.7 | JR railway |
| Geibi | JR West | 159.1 | JR railway |
| Gifu Shinai | Meitetsu | 3.7 | Tramway |
| Ginza | Tōkyō Metro | 14.3 | Metro (Subway) |
| Gomen | Tosaden | 10.9 | Tramway |
| Gonō | JR East | 147.2 | JR railway |
| Gose | Kintetsu | 5.2 | Non JR railway |
| Gotemba | JR Central | 60.2 | JR railway |
| Gotōji | JR Kyūshū | 13.3 | JR railway |
| Green - Line 4 | Yokohama Subway | 13.0 | Metro (Subway) |
| Gunchū | Iyotetsu | 11.3 | Non JR railway |
| H | Top | ||
| Hachikō | JR East | 92.0 | JR railway |
| Hachinohe | JR East | 64.9 | JR railway |
| Hachiōji | Kintetsu | 1.3 | Non JR railway |
| Haijima | Seibu | 14.3 | Non JR railway |
| Hakata-minami | JR West | 8.5 | JR railway |
| Hakodate Hon | JR Hokkaidō | 423.1 | JR railway |
| Hakodate Hon (Fujishiro) | JR Hokkaidō | 13.2 | JR railway |
| Hakodate Hon (Sawara) | JR Hokkaidō | 35.3 | JR railway |
| Hakozaki (2-gō) | Fukuoka-shi | 4.7 | Metro (Subway) |
| Hakubi | JR West | 138.4 | JR railway |
| Hakushima | Hiroden | 1.2 | Tramway |
| Hakushin | JR East | 27.3 | JR railway |
| Hanasaki | JR Hokkaidō | JR railway (Nickname) | |
| Hanawa | JR East | 106.9 | JR railway |
| Hanazono | Iyotetsu | 0.4 | Tramway |
| Hankai | Hankai | 14.1 | Tramway |
| Hanshin Namba | Hanshin | 10.1 | Non JR railway |
| Hanwa | JR West | 61.3 | JR railway |
| Hanwa (Hagoromo branch) | JR West | 1.7 | JR railway |
| Hanzōmon | Tōkyō Metro | 16.8 | Metro (Subway) |
| Hashima | Meitetsu | 1.3 | Non JR railway |
| Hibiya | Tōkyō Metro | 20.3 | Metro (Subway) |
| Hidaka Hon | JR Hokkaidō | 146.5 | JR railway |
| Higashi-Narita | Keisei | 7.1 | Non JR railway |
| Higashiyama | Nagoya-shi | 20.6 | Metro (Subway) |
| Higashiyama (Hon) | Okaden | 3.1 | Tramway |
| Himi | JR West | 16.5 | JR railway |
| Hiromi | Meitetsu | 22.3 | Non JR railway |
| Hiroshima Tankyori Kōtsū Seno | Skyrail | 1.3 | New transit system |
| Hisatsu | JR Kyūshū | 124.2 | JR railway |
| Hisatsu Orange Tetsudō | Hisatsu Orange | 116.9 | Non JR railway |
| Hitachi * | Hitachi | 18.1 | Non JR railway |
| Hitahikosan | JR Kyūshū | 68.7 | JR railway |
| Hōhi Hon | JR Kyūshū | 148.0 | JR railway |
| Hōjō | Hōjō | 13.6 | Non JR railway |
| Hokuhoku | Hokuetsu | 59.5 | Non JR railway |
| Hokuriku Hon | JR West | 353.8 | JR railway |
| Hokuriku Shinkansen | JR East | Shinkansen (Nickname) | |
| Hokusei | Sangi | 20.4 | Non JR railway |
| Hokushin | Hokushin Kyūkō | 7.5 | Non JR railway |
| Hokusō | Hokusō | 32.3 | Non JR railway |
| Hon | Keikyū | 56.7 | Non JR railway |
| Hon | Kurobe Gorge | 20.1 | Non JR railway |
| Hon | Nagasaki | 6.9 | Tramway |
| Hon | Hiroden | 5.4 | Tramway |
| Hon | Sanyō Dentetsu | 54.7 | Non JR railway |
| Hon | Hanshin | 32.1 | Non JR railway |
| Hon | Ōmi | 47.7 | Non JR railway |
| Hon | Sōtetsu | 24.6 | Non JR railway |
| Hon | Chitetsu | 53.3 | Non JR railway |
| Hon | Keisei | 69.3 | Non JR railway |
| Honmachi | Iyotetsu | 1.5 | Tramway |
| Honshi-Bisan | JR West | 12.9 | JR railway |
| Honshi-Bisan | JR Shikoku | 18.1 | JR railway |
| Hōrai - Yachigashira | Hakodate-shi | 1.4 | Tramway |
| Hotarujaya | Nagasaki | 2.2 | Tramway |
| I | Top | ||
| Ibara | Ibara | 38.3 | Non JR railway |
| Ibusuki Makurazaki | JR Kyūshū | 87.8 | JR railway |
| Ichijō-Yamahana | Sapporo-shi | 8.4 | Tramway |
| Iga | Iga | 16.6 | Non JR railway |
| Iida | JR Central | 195.7 | JR railway |
| Iiyama | JR East | 96.7 | JR railway |
| Iizaka | Fukushima | 9.2 | Non JR railway |
| Ikawa | Ōigawa | 25.5 | Non JR railway |
| Ikebukuro | Seibu | 57.8 | Non JR railway |
| Ikegami | Tōkyū | 10.9 | Non JR railway |
| Ikoma | Kintetsu | 12.4 | Non JR railway |
| Imazatosuji | Ōsaka-shi | 11.9 | Metro (Subway) |
| Imazu | Hankyū | 9.3 | Non JR railway |
| Ina (Nyū Shatoru New Shuttle) | Saitama Shin-toshi | 12.7 | New transit system |
| Inbi | JR West | 70.8 | JR railway |
| Ino | Tosaden | 11.2 | Tramway |
| Inokashira | Keiō | 12.7 | Non JR railway |
| Inuyama | Meitetsu | 26.8 | Non JR railway |
| Inuyama Monorail | Meitetsu | 1.2 | Monorail |
| Ise | Isetetsu | 22.3 | Non JR railway |
| Isesaki | Tōbu | 114.5 | Non JR railway |
| Isesaki (Oshiage) | Tōbu | 1.3 | Non JR railway |
| Ishikawa | Hokutetsu | 13.8 | Non JR railway |
| Ishinomaki | JR East | 44.9 | JR railway |
| Ishiyama Sakamoto | Keihan | 14.1 | Non JR railway |
| Isumi | Isumi | 26.8 | Non JR railway |
| Ita | Heisei Chikuhō | 16.1 | Non JR railway |
| Itami | Hankyū | 3.1 | Non JR railway |
| Itō | JR East | 16.9 | JR railway |
| Itoda | Heisei Chikuhō | 6.8 | Non JR railway |
| Itsukaichi | JR East | 11.1 | JR railway |
| Iwaizumi | JR East | 38.4 | JR railway |
| Iwate Ginga Tetsudō | IGR | 82.0 | Non JR railway |
| Izu Kyūkō | Izukyū | 45.7 | Non JR railway |
| Izumino | Sōtetsu | 11.3 | Non JR railway |
| J | Top | ||
| Jōban | JR East | 343.1 | JR railway |
| Jōetsu | JR East | 162.6 | JR railway |
| Jōetsu Shinkansen | JR East | 269.5 | Shinkansen |
| Jōetsu Shinkansen (branch) | JR East | 1.8 | Shinkansen |
| Jōhana | JR West | 29.9 | JR railway |
| Jōhoku | TKJ | 11.2 | Non JR railway |
| Jōhoku | Iyotetsu | 2.8 | Tramway |
| Jōmō | Jōmō | 25.4 | Non JR railway |
| Jōnan | Iyotetsu | 3.5 | Tramway |
| Jōshin | Jōshin | 33.7 | Non JR railway |
| Jōsō | Kantō | 51.1 | Non JR railway |
| JR Kōbe | JR West | JR railway (Nickname) | |
| JR Kyōto | JR West | JR railway (Nickname) | |
| JR Takarazuka | JR West | JR railway (Nickname) | |
| JR Tōzai | JR West | 12.5 | JR railway |
| K | Top | ||
| Kabe | JR West | 14.0 | JR railway |
| Kada | Nankai | 9.6 | Non JR railway |
| Kagoshima Hon (Mojikō - Yatsushiro) | JR Kyūshū | 232.3 | JR railway |
| Kagoshima Hon (Sendai - Kagoshima) | JR Kyūshū | 49.3 | JR railway |
| Kaigan | Kōbe Subway | 7.9 | Metro (Subway) |
| Kaikyō | JR Hokkaidō | 87.8 | JR railway |
| Kaizuka (Ex Miyajidake) | Nishitetsu | 11.0 | Non JR railway |
| Kakamigahara | Meitetsu | 17.6 | Non JR railway |
| Kakogawa | JR West | 48.5 | JR railway |
| Kamaishi | JR East | 90.2 | JR railway |
| Kameido | Tōbu | 3.4 | Non JR railway |
| Kamidaki | Chitetsu | 12.4 | Non JR railway |
| Kamiiida | Nagoya-shi | 0.8 | Metro (Subway) |
| Kamikōchi | Alpico | 14.4 | Non JR railway |
| Kamikumamoto | Kumamoto-shi | 2.9 | Tramway |
| Kamioka | Kamioka | 19.9 | Non JR railway |
| Kan | Kumamoto-shi | 3.3 | Tramway |
| Kanamachi | Keisei | 2.5 | Non JR railway |
| Kanazawa Seaside | Yokohama Shin-toshi | 10.6 | New transit system |
| Kansai Hon | JR West | 115.0 | JR railway |
| Kansai Hon | JR Central | 59.9 | JR railway |
| Kansai Kūkō (Kansai Airport) | JR West | 11.1 | JR railway |
| Karasuma | Kyōto-shi | 13.7 | Metro (Subway) |
| Karasuyama | JR East | 20.4 | JR railway |
| Karatsu | JR Kyūshū | 42.5 | JR railway |
| Kashihara | Kintetsu | 23.8 | Non JR railway |
| Kashii | JR Kyūshū | 25.4 | JR railway |
| Kashima | JR East | 17.4 | JR railway |
| Kashima * | Kashima | 27.2 | Non JR railway |
| Katamachi | JR West | 44.8 | JR railway |
| Katano | Keihan | 6.9 | Non JR railway |
| Katō (Kijima) | Nagaden | 12.9 | Non JR railway |
| Katsuyama Eiheiji | Echizen | 27.8 | Non JR railway |
| Kawagoe | JR East | 30.6 | JR railway |
| Kawaguchiko | Fujikyū | 3.0 | Non JR railway |
| Keibajō | Keiō | 0.9 | Non JR railway |
| Keihan Hon | Keihan | 49.3 | Non JR railway |
| Keihanna | Kintetsu | 18.8 | Non JR railway |
| Keihin-Tōhoku | JR East | 59.1 | JR railway (Virtual line) |
| Keiō | Keiō | 37.9 | Non JR railway |
| Keiō Shin | Keiō | 3.6 | Non JR railway |
| Keisei Narita Kūkō (Keisei Narita Airport) | Keisei | 18.1 | Non JR railway |
| Keishin | Keihan | 7.5 | Non JR railway |
| Keiyō | JR East | 43.0 | JR railway |
| Keiyō (Futamata branch) | JR East | 5.4 | JR railway |
| Keiyō (Kōya branch) | JR East | 5.9 | JR railway |
| Kengun | Kumamoto-shi | 3.0 | Tramway |
| Kesennuma | JR East | 72.8 | JR railway |
| Kibi | JR West | 20.4 | JR railway |
| Kikuchi | Kumaden | 10.8 | Non JR railway |
| Kinokuni | JR West | JR railway (Nickname) | |
| Kinugawa | Tōbu | 16.2 | Non JR railway |
| Kiryū | Tōbu | 20.3 | Non JR railway |
| Kisei Hon | JR Central | 180.2 | JR railway |
| Kisei Hon | JR West | 204.0 | JR railway |
| Kishigawa | Wakayama Dentetsu | 14.3 | Non JR railway |
| Kishin | JR West | 158.1 | JR railway |
| Kishū Tetsudō | Kitetsu | 2.7 | Non JR railway |
| Kisuki | JR West | 81.9 | JR railway |
| Kita Rias | Santetsu | 71.0 | Non JR railway |
| Kitakami | JR East | 61.1 | JR railway |
| Kitamatsue | Ichibata | 33.9 | Non JR railway |
| Kitano | Keifuku | 3.8 | Non JR railway |
| Kitto | JR Kyūshū | 61.6 | JR railway |
| Kōbe (Kōbe Hon) | Hankyū | 32.3 | Non JR railway |
| Kodomonokuni | Yokohama Kōsoku | 3.4 | Non JR railway |
| Kōentoshi | Shintetsu | 5.5 | Non JR railway |
| Koizumi (1) | Tōbu | 12.0 | Non JR railway |
| Koizumi (2) | Tōbu | 6.4 | Non JR railway |
| Kokubunji | Seibu | 7.8 | Non JR railway |
| Kokura | Kitakyūshū Kōsoku | 8.8 | Monorail |
| Kokusai-bunka-kōen-toshi | Ōsaka Monorail | 6.8 | Monorail |
| Komaki | Meitetsu | 20.6 | Non JR railway |
| Kominato Tetsudō | Kominato | 39.1 | Non JR railway |
| Kōnan | Kōnan Tetsudō | 16.8 | Non JR railway |
| Kosei | JR West | 74.1 | JR railway |
| Kotohira | Kotoden | 32.9 | Non JR railway |
| Kōtoku | JR Shikoku | 74.5 | JR railway |
| Koumi | JR East | 78.9 | JR railway |
| Kōwa | Meitetsu | 28.8 | Non JR railway |
| Kōya | Nankai | 59.9 | Non JR railway |
| Kōya (Shiomibashi) | Nankai | 4.6 | Non JR railway |
| Kōyō | Hankyū | 2.2 | Non JR railway |
| Kūkō (1-gō; Airport) | Fukuoka-shi | 13.1 | Metro (Subway) |
| Kūkō (Airport) | Meitetsu | 4.2 | Non JR railway |
| Kūkō (Airport) | Nankai | 8.8 | Non JR railway |
| Kūkō (Airport) | Keikyū | 6.5 | Non JR railway |
| Kurama | Eiden | 8.8 | Non JR railway |
| Kure | JR West | 87.0 | JR railway |
| Kurihama | Keikyū | 13.4 | Non JR railway |
| Kurihara * | Kurihara | 25.7 | Non JR railway |
| Kururi | JR East | 32.2 | JR railway |
| Kusatsu | JR West | 36.7 | JR railway |
| Kyōto | Kintetsu | 34.6 | Non JR railway |
| Kyōto (Kyōto Hon) | Hankyū | 45.3 | Non JR railway |
| Kyūdai Hon (Yufu Kōgen) | JR Kyūshū | 141.5 | JR railway |
| Kyūshū Shinkansen | JR Kyūshū | 256.8 | Shinkansen |
| L | Top | ||
| Linimo | Aichi Kōsoku | Maglev (Nickname) | |
| M | Top | ||
| Maizuru | JR West | 26.4 | JR railway |
| Marunouchi (1) | Tōkyō Metro | 24.2 | Metro (Subway) |
| Marunouchi (2) | Tōkyō Metro | 3.2 | Metro (Subway) |
| Meguro | Tōkyū | 6.5 | Non JR railway |
| Meijō | Nagoya-shi | 26.4 | Metro (Subway) |
| Meikō | Nagoya-shi | 6.0 | Metro (Subway) |
| Meishō | JR Central | 43.5 | JR railway |
| Midōsuji | Ōsaka-shi | 24.5 | Metro (Subway) |
| Mikawa | Meitetsu | 39.8 | Non JR railway |
| Miki | Miki | 6.6 | Non JR railway |
| Mikuni Awara | Echizen | 25.2 | Non JR railway |
| Minami (Hijiyama) | Hiroden | 2.5 | Tramway |
| Minami Rias | Santetsu | 36.6 | Non JR railway |
| Minami-Ōsaka | Kintetsu | 39.8 | Non JR railway |
| Minato | Hitachinaka Kaihin | 14.3 | Non JR railway |
| Minatomirai21 | Yokohama Kōsoku | 4.1 | Non JR railway |
| Mine | JR West | 46.0 | JR railway |
| Minobu | JR Central | 88.4 | JR railway |
| Minomachi | Meitetsu | 18.8 | Non JR railway |
| Minoo | Hankyū | 4.0 | Non JR railway |
| Misumi | JR Kyūshū | 25.6 | JR railway |
| Mita | TOEI | 24.2 | Metro (Subway) |
| Mito | JR East | 50.2 | JR railway |
| Miyafuku | Kitakinki Tango | 30.4 | Non JR railway |
| Miyajima | Hiroden | 16.1 | Non JR railway |
| Miyazaki-kūkō | JR Kyūshū | 1.4 | JR railway |
| Miyazu | Kitakinki Tango | 83.6 | Non JR railway |
| Mizuma | Mizuma | 5.5 | Non JR railway |
| Mizushima Hon | Mizushima Rinkai | 10.4 | Non JR railway |
| Mōka | Mōka | 41.9 | Non JR railway |
| Mugi | JR Shikoku | 79.3 | JR railway |
| Mukogawa | Hanshin | 1.7 | Non JR railway |
| Muroran Hon | JR Hokkaidō | 211.0 | JR railway |
| Muroran Hon (Branch) | JR Hokkaidō | 7.0 | JR railway |
| Musashino | JR East | 71.8 | JR railway |
| Myōken | Noseden | 12.2 | Non JR railway |
| N | Top | ||
| Nagahori Tsurumi-ryokuchi | Ōsaka-shi | 15.0 | Metro (Subway) |
| Nagano | Kintetsu | 12.5 | Non JR railway |
| Nagano (Hon) | Nagaden | 33.2 | Non JR railway |
| Nagano Shinkansen | JR East | 117.4 | Shinkansen |
| Nagao | Kotoden | 14.6 | Non JR railway |
| Nagareyama | Ryūtetsu | 5.7 | Non JR railway |
| Nagasaki Hon | JR Kyūshū | 125.3 | JR railway |
| Nagasaki Hon (Old line) | JR Kyūshū | 23.5 | JR railway |
| Nagoya | Kintetsu | 78.8 | Non JR railway |
| Nagoya Hon | Meitetsu | 99.8 | Non JR railway |
| Nakamura | Tosa Kuroshio | 43.0 | Non JR railway |
| Nakanoshima | Keihan | 3.0 | Non JR railway |
| Namba | Kintetsu | 2.0 | Non JR railway |
| Namboku | Sapporo-shi | 14.3 | Metro (Subway) |
| Namboku | Kōbe Rapid | 0.4 | Non JR railway |
| Namboku | Kitakyū | 5.9 | Non JR railway |
| Namboku | Tōkyō Metro | 21.3 | Metro (Subway) |
| Namboku | Sendai-shi | 14.8 | Metro (Subway) |
| Nambu | JR East | 35.5 | JR railway |
| Nambu (branch) | JR East | 4.1 | JR railway |
| Nanakuma (3-gō) | Fukuoka-shi | 12.0 | Metro (Subway) |
| Nanao | JR West | 59.5 | JR railway |
| Nanao | Noto | 28.0 | Non JR railway |
| Nankai Hon | Nankai | 64.2 | Non JR railway |
| Nankō Port Town | Ōsaka-shi | 7.9 | New transit system |
| Nara | Kintetsu | 26.7 | Non JR railway |
| Nara | JR West | 34.7 | JR railway |
| Narita | JR East | 75.4 | JR railway |
| Narita (Abiko) | JR East | 32.9 | JR railway |
| Narita (Kūkō Airport) | JR East | 10.8 | JR railway |
| Narita Sky Access | Keisei | Non JR railway (Virtual line) | |
| Naruto | JR Shikoku | 8.5 | JR railway |
| Negishi | JR East | 22.1 | JR railway |
| Nemuro Hon | JR Hokkaidō | 443.8 | JR railway |
| Nichinan | JR Kyūshū | 88.9 | JR railway |
| Nikkō | JR East | 40.5 | JR railway |
| Nikkō | Tōbu | 94.5 | Non JR railway |
| Nippō Hon | JR Kyūshū | 462.6 | JR railway |
| Nippori-Toneri Liner | TOEI | 9.7 | New transit system |
| Nishikigawa Seiryū | Nishikigawa | 32.7 | Non JR railway |
| Nishi-kyūshū | Matsuura | 93.8 | Non JR railway |
| Nishi-Nagoyakō | Nagoya Rinkai | 15.2 | Non JR railway |
| Nishio | Meitetsu | 24.7 | Non JR railway |
| Nissei | Noseden | 2.6 | Non JR railway |
| Noda | Tōbu | 62.7 | Non JR railway |
| Noto | Noto | 61.0 | Non JR railway |
| O | Top | ||
| Ōarai Kashima | Kashima Rinkai | 53.0 | Non JR railway |
| Obama | JR West | 84.3 | JR railway |
| Odawara | Odakyū | 82.5 | Non JR railway |
| Ōedo | TOEI | 40.7 | Metro (Subway) |
| Ōfunato | JR East | 105.7 | JR railway |
| Oga | JR East | 26.6 | JR railway |
| Ogose | Tōbu | 10.9 | Non JR railway |
| Ōhata | Shimokita Kōtsū | 18.0 | Non JR railway |
| Ōigawa Hon | Ōigawa | 39.5 | Non JR railway |
| Ōimachi | Tōkyū | 10.4 | Non JR railway |
| Ōito | JR East | 70.1 | JR railway |
| Ōito | JR West | 35.3 | JR railway |
| Okinawa Toshi Monorail | Okinawa Monorail | 12.8 | Monorail |
| Ōme | JR East | 37.2 | JR railway |
| Ōminato | JR East | 58.4 | JR railway |
| Ōmura | JR Kyūshū | 47.6 | JR railway |
| Onoda | JR West | 11.6 | JR railway |
| Onoda (Motoyama branch) | JR West | 2.3 | JR railway |
| Ōsaka | Kintetsu | 108.9 | Non JR railway |
| Ōsaka Higashi | JR West | 9.2 | JR railway |
| Ōsaka kanjō (loop) | JR West | 20.7 | JR railway |
| Ōsaka monorail | Ōsaka Monorail | 21.2 | Monorail |
| Oshiage | Keisei | 5.7 | Non JR railway |
| Ōtemachi | Iyotetsu | 1.4 | Tramway |
| Ōtō | Keihan | 2.3 | Non JR railway |
| Ōtsuki | Fujikyū | 23.6 | Non JR railway |
| Ōu Hon (Akita - Aomori) | JR East | 185.8 | JR railway |
| Ōu Hon (Shinjō - Akita) | JR East | 150.1 | JR railway |
| Ōu Hon [Yamagata] (Fukushima - Shinjō ) | JR East | 148.6 | JR railway |
| Ōura | Nagasaki | 1.1 | Tramway |
| Ōwani | Kōnan Tetsudō | 13.9 | Non JR railway |
| P | Top | ||
| Port Island (Portliner) | Kōbe New Transit | 8.2 | New transit system |
| Port Island (Portliner [Loop]) | Kōbe New Transit | 2.6 | New transit system |
| R | Top | ||
| Rikuu-sai | JR East | 43.0 | JR railway |
| Rikuu-tō | JR East | 94.1 | JR railway |
| Rinkai | TWR | 12.2 | Non JR railway |
| Rokkō Island (Rokkōliner) | Kōbe New Transit | 4.5 | New transit system |
| Rumoi Hon | JR Hokkaidō | 66.8 | JR railway |
| Ryōmō | JR East | 84.4 | JR railway |
| Ryūgasaki | Kantō | 4.5 | Non JR railway |
| S | Top | ||
| Sagami | JR East | 33.3 | JR railway |
| Sagamihara | Keiō | 22.6 | Non JR railway |
| Sagano | JR West | JR railway (Nickname) | |
| Sagano Kankō | Sagano Scenic | 7.3 | Tourist |
| Saikyō | JR East | 36.9 | JR railway (Virtual line) |
| Saitama Kosoku Tetsudō | Saitama | 14.6 | Non JR railway |
| Saito | Ōsaka Monorail | Monorail (Nickname) | |
| Sakai | JR West | 17.9 | JR railway |
| Sakaisuji | Ōsaka-shi | 8.5 | Metro (Subway) |
| Sakuradōri | Nagoya-shi | 14.9 | Metro (Subway) |
| Sakurai | JR West | 29.4 | JR railway |
| Sakurajima | JR West | 4.1 | JR railway |
| Sakuramachi | Nagasaki | 0.9 | Tramway |
| Sanbashi | Tosaden | 3.2 | Tramway |
| Sanda | Shintetsu | 12.0 | Non JR railway |
| Sangi | Sangi | 26.6 | Non JR railway |
| Sangū | JR Central | 29.1 | JR railway |
| Sanin Hon | JR West | 673.8 | JR railway |
| Sanin Hon (Senzaki branch) | JR West | 2.2 | JR railway |
| Sankō | JR West | 108.1 | JR railway |
| Sano | Tōbu | 22.1 | Non JR railway |
| Sanyō Hon | JR Kyūshū | 6.3 | JR railway |
| Sanyō Hon | JR West | 528.1 | JR railway |
| Sanyō Hon (Wadamisaki) | JR West | 2.7 | JR railway |
| Sanyō Shinkansen | JR West | 553.7 | Shinkansen |
| Sasaguri | JR Kyūshū | 25.1 | JR railway |
| Sasebo | JR Kyūshū | 48.8 | JR railway |
| Sasshō | JR Hokkaidō | 76.5 | JR railway |
| Sayama | Seibu | 4.2 | Non JR railway |
| Seibuen | Seibu | 2.4 | Non JR railway |
| Seikibashi | Okaden | 1.6 | Tramway |
| Seishin-Yamate | Kōbe Subway | 22.7 | Metro (Subway) |
| Sekihoku Hon | JR Hokkaidō | 234.0 | JR railway |
| Sekishō | JR Hokkaidō | 132.4 | JR railway |
| Sekishō (Yūbari branch) | JR Hokkaidō | 16.1 | JR railway |
| Semboku Kōsoku Tetsudō | OTK | 14.3 | Non JR railway |
| Sendai Kūkō | Sendai Airport Transit | 7.1 | Non JR railway |
| Senmō Hon | JR Hokkaidō | 166.2 | JR railway |
| Sennichimae | Ōsaka-shi | 13.1 | Metro (Subway) |
| Senri | Hankyū | 13.6 | Non JR railway |
| Senseki | JR East | 50.2 | JR railway |
| Senzan | JR East | 58.0 | JR railway |
| Setagaya | Tōkyū | 5.0 | Tramway |
| Seto | Meitetsu | 20.6 | Non JR railway |
| Seto-Ōhashi | Shared | JR railway (Nickname) | |
| Shibayama Tetsudō | Shibayama | 2.2 | Non JR railway |
| Shido | Kotoden | 12.5 | Non JR railway |
| Shigaraki | Shigaraki Kōgen | 14.7 | Non JR railway |
| Shigi | Kintetsu | 2.8 | Non JR railway |
| Shima | Kintetsu | 24.5 | Non JR railway |
| Shimabara Tetsudō | Shimabara | 43.2 | Non JR railway |
| Shinano Tetsudō | Shinano | 65.1 | Non JR railway |
| Shinetsu Hon (Shinonoi - Niigata) | JR East | 220.6 | JR railway |
| Shinetsu Hon (Takasaki - Yokokawa) | JR East | 29.7 | JR railway |
| Shinjuku | Seibu | 47.5 | Non JR railway |
| Shinjuku | TOEI | 23.5 | Metro (Subway) |
| Shin-Keisei | Shin-Keisei | 26.5 | Non JR railway |
| Shinminatokō | Manyō | 4.9 | Non JR railway |
| Shinonoi | JR East | 66.7 | JR railway |
| Shizuoka-Shimizu | Shizuoka | 11.0 | Non JR railway |
| Shōnan-Shinjuku Line | JR East | JR railway (Virtual line) | |
| Skyrail Midorizaka | Skyrail | New transit system (Nickname) | |
| Sōbu Hon (Chiba - Chōshi) | JR East | 81.3 | JR railway |
| Sōbu Hon (Ochanomiya - Kinshichō) | JR East | 4.3 | JR railway |
| Sōbu Hon (Tōkyō - Chiba) | JR East | 39.2 | JR railway |
| Sotobō | JR East | 93.3 | JR railway |
| Sōya Hon | JR Hokkaidō | 259.4 | JR railway |
| Suigun | JR East | 137.5 | JR railway |
| Suigun (Hitachi-Ōta branch) | JR East | 9.5 | JR railway |
| Suizenji | Kumamoto-shi | 2.4 | Tramway |
| Sukumo | Tosa Kuroshio | 23.6 | Non JR railway |
| Sunzu | Izu Hakone | 19.8 | Non JR railway |
| Suzuka | Kintetsu | 8.2 | Non JR railway |
| T | Top | ||
| Tadami | JR East | 135.2 | JR railway |
| Taga | Ōmi | 2.5 | Non JR railway |
| Tagami | Meitetsu | 1.4 | Non JR railway |
| Tagawa | Heisei Chikuhō | 26.3 | Non JR railway |
| Taisha | Ichibata | 8.3 | Non JR railway |
| Taita | JR Central | 17.8 | JR railway |
| Takachiho | Takachiho | 50.0 | Non JR railway |
| Takahama | Iyotetsu | 9.4 | Non JR railway |
| Takamori | Minami-Aso | 17.7 | Non JR railway |
| Takao | Keiō | 8.6 | Non JR railway |
| Takaoka kidō | Manyō | 7.9 | Tramway |
| Takarazuka (Takarazuka Hon) | Hankyū | 24.5 | Non JR railway |
| Takasaki | JR East | 74.7 | JR railway |
| Takashinohama | Nankai | 1.5 | Non JR railway |
| Takayama Hon | JR West | 36.6 | JR railway |
| Takayama Hon | JR Central | 189.2 | JR railway |
| Takehana | Meitetsu | 10.3 | Non JR railway |
| Taketoyo | JR Central | 19.3 | JR railway |
| Tama | Odakyū | 10.6 | Non JR railway |
| Tama Toshi Monorēru | Tama Monorail | 16.0 | Monorail |
| Tamagawa | Seibu | 8.0 | Non JR railway |
| Tamako | Seibu | 9.2 | Non JR railway |
| Tanagawa | Nankai | 2.6 | Non JR railway |
| Tanimachi | Ōsaka-shi | 28.1 | Metro (Subway) |
| Taniyama | Kagoshima-shi | 6.4 | Tramway |
| Tarumi | Tarumi | 34.5 | Non JR railway |
| Tasaki | Kumamoto-shi | 0.6 | Tramway |
| Tateyama | Chitetsu | 24.2 | Non JR railway |
| Tawaramoto | Kintetsu | 10.1 | Non JR railway |
| Tazawako | JR East | 75.6 | JR railway |
| Tenjin Ōmuta | Nishitetsu | 74.8 | Non JR railway |
| Tenri | Kintetsu | 4.5 | Non JR railway |
| Tenryū Hamanako | Tenryū Hamanako | 67.7 | Non JR railway |
| Tetsudō | Hakone Tozan | 15.0 | Non JR railway |
| Toba | Kintetsu | 13.2 | Non JR railway |
| Tōbu Kyūryō | Aichi Kōsoku | 8.9 | Maglev |
| Toden Arakawa | TOEI | 12.2 | Tramway |
| Tōgane | JR East | 13.8 | JR railway |
| Tōhō | Sapporo-shi | 13.6 | Metro (Subway) |
| Tōhoku Hon (Akabane - Musashi-Urawa - Ōmiya) | JR East | 18.0 | JR railway |
| Tōhoku Hon (Kuroiso - Sendai) | JR East | 188.5 | JR railway |
| Tōhoku Hon (Rifu branch) | JR East | 4.2 | JR railway |
| Tōhoku Hon (Sendai - Morioka) | JR East | 183.5 | JR railway |
| Tōhoku Hon (Tōkyō - Kuroiso) | JR East | 163.3 | JR railway |
| Tōhoku Hon (via Oku) | JR East | 7.6 | JR railway |
| Tōhoku Shinkansen | JR East | 674.9 | Shinkansen |
| Tōjō Hon | Tōbu | 75.0 | Non JR railway |
| Tōkadai | Tōkadai | 7.4 | New transit system |
| Tōkaidō Hon (Atami - Maibara) | JR Central | 341.3 | JR railway |
| Tōkaidō Hon (Hinkaku line) | JR East | 17.8 | JR railway |
| Tōkaidō Hon (Maibara - Kōbe) | JR West | 143.6 | JR railway |
| Tōkaidō Hon (Mino-Akasaka branch) | JR Central | 5.0 | JR railway |
| Tōkaidō Hon (Tōkyō - Atami) | JR East | 104.6 | JR railway |
| Tōkaidō Hon (Umeda Kamotsu Umeda Freight) | JR West | 4.7 | JR railway |
| Tōkaidō Shinkansen | JR Central | 515.4 | Shinkansen |
| Tokoname | Meitetsu | 29.3 | Non JR railway |
| Tokushima | JR Shikoku | 67.5 | JR railway |
| Tōkyō Monorail Haneda | Tōkyō Monorail | 17.8 | Monorail |
| Tōkyū Tamagawa | Tōkyū | 5.6 | Non JR railway |
| Toshima | Seibu | 1.0 | Non JR railway |
| Toso | Kagoshima-shi | 2.7 | Tramway |
| Towadakankō Dentetsu | Towadakankō | 14.7 | Non JR railway |
| Town-liner Line 1 (1-gō) | Chiba Monorail | 3.2 | Monorail |
| Town-liner Line 2 (2-gō) | Chiba Monorail | 12.0 | Monorail |
| Toyama shinai kidō | Chitetsu | 6.4 | Tramway |
| Toyama toshin (Kanjō) | Chitetsu | 0.9 | Tramway |
| Toyamakō (Portram) | Toyama Light Rail | 7.6 | Non JR railway |
| Tōyō Kōsoku | Tōyō Kōsoku | 16.2 | Non JR railway |
| Toyokawa | Meitetsu | 7.2 | Non JR railway |
| Tōyoko | Tōkyū | 24.2 | Non JR railway |
| Toyota | Meitetsu | 15.2 | Non JR railway |
| Tōzai | Tōkyō Metro | 30.8 | Metro (Subway) |
| Tōzai | Kyōto-shi | 17.5 | Metro (Subway) |
| Tōzai | Sapporo-shi | 20.1 | Metro (Subway) |
| Tōzai (Hankyū Sannomiya - Nishidai) | Kōbe Rapid | 5.7 | Non JR railway |
| Tōzai (Motomachi -Kōsoku Kōbe) | Kōbe Rapid | 1.5 | Non JR railway |
| Tsugaru | JR East | 55.8 | JR railway |
| Tsugaru Tetsudō | Tsutetsu | 20.7 | Non JR railway |
| Tsugaru-Kaikyō | Shared | JR railway (Nickname) | |
| Tsukuba Express | MIR | 58.3 | Non JR railway |
| Tsurumai | Nagoya-shi | 20.4 | Metro (Subway) |
| Tsurumi | JR East | 7.0 | JR railway |
| Tsurumi (Ōkawa branch) | JR East | 1.0 | JR railway |
| Tsurumi (Umi-Shibaura branch) | JR East | 1.7 | JR railway |
| Tsushima | Meitetsu | 11.8 | Non JR railway |
| Tsuyama | JR West | 58.7 | JR railway |
| U | Top | ||
| Ube | JR West | 33.2 | JR railway |
| Uchibō | JR East | 119.4 | JR railway |
| Uchiko | JR Shikoku | 5.3 | JR railway |
| Uemachi | Hankai | 4.6 | Tramway |
| Uetsu Hon | JR East | 271.7 | JR railway |
| Uji | Keihan | 7.6 | Non JR railway |
| Ujina | Hiroden | 5.7 | Tramway |
| Uno | JR West | 32.8 | JR railway |
| Utsube | Kintetsu | 5.7 | Non JR railway |
| Utsunomiya | JR East | JR railway (Nickname) | |
| Utsunomiya | Tōbu | 24.3 | Non JR railway |
| W | Top | ||
| Wakasa | Wakasa | 19.2 | Non JR railway |
| Wakayama | JR West | 87.5 | JR railway |
| Wakayamakō | Nankai | 2.8 | Non JR railway |
| Watarase Keikoku | Watetsu | 44.1 | Non JR railway |
| Y | Top | ||
| Yahiko | JR East | 17.4 | JR railway |
| Yamada | Kintetsu | 28.3 | Non JR railway |
| Yamada | JR East | 157.5 | JR railway |
| Yamagata Shinkansen | JR East | Shinkansen | |
| Yamaguchi | Seibu | 2.8 | New transit system |
| Yamaguchi | JR West | 93.9 | JR railway |
| Yamanote | JR East | 20.6 | JR railway |
| Yamatoji | JR West | JR railway (Nickname) | |
| Yashiro | Nagaden | 24.4 | Non JR railway |
| Yodo | JR Shikoku | 76.3 | JR railway |
| Yōkaichi | Ōmi | 9.3 | Non JR railway |
| Yokogawa | Hiroden | 1.4 | Tramway |
| Yokogawara | Iyotetsu | 13.2 | Non JR railway |
| Yokohama | JR East | 42.6 | JR railway |
| Yokosuka | JR East | 23.9 | JR railway |
| Yonesaka | JR East | 90.7 | JR railway |
| Yōrō | Yōrō | 57.5 | Non JR railway |
| Yosan | JR Shikoku | 297.6 | JR railway |
| Yosan (1) | JR Shikoku | 23.5 | JR railway |
| Yosan (2) | JR Shikoku | 5.9 | JR railway |
| Yoshino | Kintetsu | 25.2 | Non JR railway |
| Yotsubashi | Ōsaka-shi | 11.4 | Metro (Subway) |
| Yui Rail | Okinawa Monorail | Monorail (Nickname) | |
| Yūkarigaoka | Yamaman | 4.1 | New transit system |
| Yunokawa - Ōmori - Hon | Hakodate-shi | 9.3 | Tramway |
| Yunomae | Kumagawa | 24.8 | Non JR railway |
| Yunoyama | Kintetsu | 15.4 | Non JR railway |
| Yūrakuchō | Seibu | 2.6 | Non JR railway |
| Yūrakuchō | Tōkyō Metro | 20.0 | Metro (Subway) |
| Yurikamome | Yurikamome | 14.7 | New transit system |
| Z | Top | ||
| Zushi | Keikyū | 5.9 | Non JR railway |