| Train name | Name meaning | Operator | Train endpoints | Operated |
| A-Train | refers to Ariake region | JR Kyushu | Yoshizuka, Hakata – Nagasu | 1967– |
| Aizu Liner | refers to Aizu region | JR East | Kōriyama – Aizu-Wakamatsu | 1968– |
| Akagi / Swallow Akagi | refers to Mt. Akagi | JR East | Ueno, Shinjuku – Takasaki, Maebashi | 1982– |
| Ariake | refers to Ariake region | JR Kyushu | Kumamoto – Misumi | 1967–2021 |
| Asagiri | Morning mist | Odakyu / JR Central | Shinjuku – Gotemba | 1991–2018 |
| Ashizuri | refers to Cape Ashizuri | JR Shikoku | Kōchi – Nakamura | 1990– |
| Ayame | Japanese iris | JR East | Tokyo – Narita, Kashimajingū, Chōshi | 1975–2015 |
| Azusa | refers to Azusa River | JR East | Shinjuku, Tokyo, Chiba – Matsumoto, Hakuba | 1966– |
| Banetsu Monogatari | refers to Banetsu West Line | JR East | Niigata - Aizu-Wakamatsu | 1999– |
| Dinostar | portmanteau derived from the English word "dinosaur" for which Fukui is famous and the word "star"[4] | JR-West | Fukui – Kanazawa | 2015–2024 |
| Enoshima | refers to Enoshima | Odakyu | Shinjuku – Fujisawa – Katase-Enoshima | 1964– |
| Fuji Excursion | | JR East | Shinjuku – Kawaguchiko | 2019– |
| Fujikawa | refers to Fuji River | JR Central | Kōfu – Shizuoka | 1996– |
| Hachiōji / Ōme | | JR East | Tokyo – Hachiōji,Ōme | 2019–2025 |
| Hakone / Super Hakone / Metro Hakone | refers to Hakone | Odakyu | Shinjuku, Kita-Senju – Hakone-Yumoto | 1950– |
| Hakuchō / Super Hakuchō | Swan | JR East / JR Hokkaido | Shin-Aomori, Aomori – Hakodate | 2002–2016 |
| Hamakaze | Sea breeze/beach wind | JR-West | Ōsaka – Kasumi, Hamasaka, Tottori | 1972– |
| Haruka | Faraway | JR-West | Kyoto/Shin-Ōsaka – Kansai Airport | 1993– |
| Hashidate | - | JR-West, Willer Trains | Kyoto – Amanohashidate, Toyooka | 1965– |
| Hida | refers to Hida | JR Central | Ōsaka, Nagoya – Takayama, Hida Furukawa, Toyama | 1968– |
| Hitachi | old name of Ibaraki Prefecture | JR East | Shinagawa – Sendai | 1969– |
| Hitoyoshi | name of Hitoyohi, Kumamoto | JR Kyushu | Kumamoto – Hitoyoshi | 2009–2024 |
| Hokuto | Big Dipper | JR Hokkaido | Hakodate – Sapporo | 1965– |
| Homeway / Metro Homeway | - | Odakyu | Shinjuku, Kita-Senju, Ōtemachi – Machida, Sagami-Ōno, Hon-Atsugi, Odawara, Hakone-Yumoto, Karakida, Fujisawa, Katase-Enoshima | 1999– |
| Huis Ten Bosch | - | JR Kyushu | Hakata – Huis Ten Bosch | 1992– |
| Inaho | Rice stalk | JR East | Niigata – Sakata, Akita | 1969– |
| Inaji | Way to Ina, refers to Ina region | JR Central | Toyohashi – Iida | 1996– |
| Ishizuchi | Refers to Mt. Ishizuchi | JR Shikoku | Takamatsu – Matsuyama | 1988– |
| Iyonada Monogatari | Story of the Iyonada Sea; refers to Iyo, old name of Ehime Prefecture | JR Shikoku | Matsuyama – Iyo-Ōzu, Yawatahama | 2014– |
| Kaiji | Way to Kai, old name of Yamanashi Prefecture | JR East | Tokyo, Shinjuku – Kōfu, Ryūō | 1988– |
| Kaio | refers to Kaiō Hiroyuki, a celebrity sumo wrestler from Nōgata | JR Kyushu | Hakata – Nōgata | 2001– |
| Kamome | Seagull | JR Kyushu | Hakata – Saga, Hizen-Kashima, Nagasaki and Haiki – Nagasaki | 1961– |
| Kamoshika | Japanese serow | JR East | Akita – Aomori | 1997–2010 |
| Kamui | Kamuy | JR Hokkaido | Sapporo – Asahikawa | 2007– |
| Kawasemi Yamasemi | refers to kingfishers native to the area | JR Kyushu | Kumamoto-Hitoyoshi | 2017- |
| Kinosaki | refers to Kinosaki Onsen | JR-West | Kyoto – Kinosaki Onsen | 1996– |
| Kinugawa / Spacia Kinugawa | refers to Kinugawa River | JR East / Tobu Railway | Shinjuku – Kinugawa-Onsen | 2006– |
| Kirameki | Glitter | JR Kyushu | Hakata – Kokura, Mojikō | 2001– |
| Kirishima | refers to Mt. Kirishima | JR Kyushu | Miyazaki – Miyakonojō, Nishi-Miyakonojō, Kagoshima-Chūō and Kokubu – Kagoshima-Chūō | 1995– |
| Kita-Kinki | North Kinki | JR-West | Shin-Ōsaka, Fukuchiyama – Toyooka, Kinosaki Onsen | 1986–2011 |
| Kounotori | Stork | JR-West | Shin-Ōsaka – Fukuchiyama, Toyooka, Kinosaki Onsen | 2011– |
| Kumagawa | refers to Kuma River | JR Kyushu | Kumamoto – Hitoyoshi | 2004– |
| Kuroshio | Kuroshio Current | JR-West | Kyoto, Shin-Ōsaka, Tennōji – Wakayama, Shirahama, Shingu | 1965– |
| Kusatsu/Shima | refers to Kusatsu Onsen | JR East | Ueno – Naganoharakusatsuguchi | 1985– |
| Lilac | - | JR Hokkaido | Sapporo – Asahikawa | 1980–2007; 2017– |
| Mahoroba,Rakuraku Yamato | | JR West | Osaka,Shin-Ōsaka – Nara | Mahoroba: 2010;2019- Rakuraku Yamato: 2024- |
| Midori | Green | JR Kyushu | Hakata – Sasebo | 1976– |
| Muroto | refers to Cape Muroto | JR Shikoku | Tokushima – Mugi | 1962-2025 |
| Nanki | refers to South Kii Peninsula | JR Central | Nagoya – Shingū, Kii-Katsuura | 1978– |
| Nanpū | Southern wind | JR Shikoku | Okayama – Kōchi | 1972– |
| Narita Express | - | JR East | Tokyo area – Narita Airport | 1991– |
| Nikkō / Spacia Nikkō | refers to Nikkō | JR East / Tōbu | Shinjuku – Tōbu-Nikko | 2006– |
| Noto Kagaribi | Noto fire built in an iron basket | JR-West | Kanazawa – Wakuraonsen | 2015– |
| Odoriko / Super View Odoriko / Saphir Odoriko | refers to The Dancing Girl of Izu | JR East / Izukyū / Izuhakone Railway | Tokyo, Shinjuku, Ikebukuro – Itō, Izukyū Shimoda, Shuzenji | Odoriko: 1981- Super View Odoriko: 1990–2020 Saphir Odoriko: 2020- |
| Ohayo Express / Oyasumi Express | Good morning express / Good night express | JR-West | Tsuruga – Kanazawa | - Ohayo Express: 2001–2024
- Oyasumi Express: 2004–2024
|
| Ohayo Tochigi / Hometown Tochigi | Good morning Tochigi / - | JR East | Shinjuku – Utsunomiya, Kuroiso | 1995–2010 |
| Okhotsk | refers to Sea of Okhotsk | JR Hokkaido | Sapporo – Asahikawa - Abashiri | 1972– |
| Ozora | Sky | JR Hokkaido | Sapporo – Kushiro | 1961– |
| Rakuraku Biwako | | JR West | Osaka – Kusatsu,Maibara | 2003- |
| Rakuraku Harima | | JR West | Kyoto,Shin-Ōsaka – Aboshi | 2019- |
| Relay Tsubame | Swallow | JR Kyushu | Hakata – Shin-Yatsushiro | 2004–2011 |
| Relay Kamome | - | JR Kyushu | Hakata - Takeo-Onsen | 2023- |
| Sagami / Metro Sagami | refers to Sagami, old name of Kanagawa Prefecture | Odakyu | Shinjuku, Kita-Senju – Machida, Sagami-Ōno, Hon-Atsugi, Odawara | 1950– |
| Sarobetsu | refers to Sarobetsu plain | JR Hokkaido | Asahikawa – Wakkanai | 2017– |
| Sazanami | Ripples | JR East | Tokyo – Kimitsu | 1972– |
| Shimanto | refers to Shimanto River | JR Shikoku | Takamatsu – Kōchi, Sukumo | 1988– |
| Shinano | refers to Shinano region, old name of Nagano Prefecture | JR Central | Nagoya – Nagano | 1968– |
| Shiokaze | Sea breeze | JR Shikoku | Okayama – Imabari, Matsuyama | 1972– |
| Shiosai | - | JR East | Tokyo, Shinjuku – Sakura, Narutō, Chōshi | 1975– |
| Shirasagi | Egret | JR-West | Nagoya, Maibara – Tsuruga | 1964– |
| Shirayuki | White snow | JR East | Niigata – Jōetsumyōkō,Arai | 2015– |
| Shōnan | refers to Shōnan region | JR East | Tokyo,Shinjyuku – Hiratsuka,Odawara | 2021– |
| Skyliner | - | Keisei | Keisei Ueno – Narita Airport | 1972– |
| Sonic | - | JR Kyushu | Hakata – Yanagigaura, Ōita, Saiki (via Nippō Main Line) | 1997– |
| Soya | refers to Soya region | JR Hokkaido | Sapporo – Asahikawa - Wakkanai | 2000– |
| Super Hakuto | White hare, i.e. Hare of Inaba | JR-West, Chizu Express | Kyoto – Tottori - Kurayoshi | 1994– |
| Super Inaba | refers to Inaba, old name of Tottori Prefecture. Also Hare of Inaba | JR-West, Chizu Express | Okayama – Tottori | 1993– |
| Super Matsukaze | Pine wind | JR-West | Tottori – Masuda | 2003– |
| Super Oki | refers to Oki Islands | JR-West | Tottori – Yonago, Shin-Yamaguchi | 2001– |
| Super White Arrow | - | JR Hokkaido | New Chitose Airport, Sapporo – Asahikawa | 1986–2007 |
| Suzuran | Lily of the valley | JR Hokkaido | Muroran – Sapporo | 1992– |
| Taisetsu | another name of Mt. Daisetsu | JR Hokkaido | Asahikawa - Abashiri | 2017–2025 |
| Thunderbird | - | JR-West | Ōsaka – Tsuruga | 1995– |
| Tokachi | refers to Tokachi region | JR Hokkaido | Sapporo – Obihiro | 1990– |
| Tōkai | refers to Tokai region | JR Central | Tokyo – Shizuoka | 1996–2007 |
| Tokiwa | old name of Ibaraki Prefecture | JR East | Shinagawa – Tsuchiura, Katsuta, Iwaki, Takahagi | 2015– |
| Trans-Kyushu Limited Express | - | JR Kyushu | Beppu – Hitoyoshi, Kumamoto | 2004– |
| Tsugaru | old name of Aomori Prefecture | JR East | Akita – Aomori | 2002– |
| Tsurugisan | refers to Mount Tsurugi | JR Shikoku | Tokushima – Awa-ikeda | 1996– |
| Umisachi Yamasachi | refers to Hoderi, whose myth supposedly takes place in Southern Kyushu | JR Kyushu | Miyazaki-Nangō | 2009- |
| Uwakai | refers to Sea of Uwa | JR Shikoku | Matsuyama – Uwajima | 1990– |
| Uzushio | refers to Naruto whirlpools | JR Shikoku | Takamatsu – Tokushima | 1988– |
| Wakashio | Growing tide from neap tide to spring tide, also another name of Kuroshio Current | JR East | Shinjuku – Kazusa-Ichinomiya, Katsuura, Awa-Kamogawa | 1972– |
| Yakumo | thick clouds | JR-West | Okayama – Izumoshi | 1972– |
| Yufu / Yufuin-no-mori | refers to Yufu Onsen | JR Kyushu | Hakata – Yufuin, Ōita, Beppu (via Kyūdai Main Line) | 1989– |
| μ Sky | - | Meitetsu | Shin-Unuma, Shin-Kani, Mikakino, Meitetsu Gifu, Meitetsu Nagoya – Central Japan International Airport | 2005– |