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| Sagami-ono | ODAKYU | Odawara line | Kanagawa pref. | 相模大野 | 神奈川県 | |
| Sagami-ono | ODAKYU | Enoshima line | Kanagawa pref. | 相模大野 | 神奈川県 | |
| Saginomiya | SEIBU | Seibu-shinjuku line | Nakano ward | SS09 | 鷺ノ宮 | 中野区 |
| Saginuma | TOKYU | Denen-toshi line | Kanagawa pref. | DT14 | 鷺沼 | 神奈川県 |
| Saitama-shintoshin | JR East | Keihin-tohoku line | Saitama pref. | さいたま新都心 | 埼玉県 | |
| Saitama-shintoshin | JR East | Takasaki line | Saitama pref. | さいたま新都心 | 埼玉県 | |
| Saitama-shintoshin | JR East | Tohoku line/Utsunomiya line | Saitama pref. | さいたま新都心 | 埼玉県 | |
| Sakado | TOBU | Tojo line | Saitama pref. | TJ-26 | 坂戸 | 埼玉県 |
| Sakado | TOBU | Ogose line | Saitama pref. | TJ-26 | 坂戸 | 埼玉県 |
| Sakaecho | TOEI | Arakawa line | Kita ward | 栄町 | 北区 | |
| Sakaimachi | TOBU | Isesaki line | Gunma pref. | TI-22 | 境町 | 群馬県 |
| Sakudaira | JR East | Nagano shinkansen | Nagano pref. | 佐久平 | 長野県 | |
| Sakura | JR East | Sobu line | Chiba pref. | 佐倉 | 千葉県 | |
| Sakura | JR East | Narita line | Chiba pref. | 佐倉 | 千葉県 | |
| Sakura-jyosui | KEIO | Keio line | Setagaya ward | KO08 | 桜上水 | 世田谷区 |
| Sakura-shinmachi | TOKYU | Denen-toshi line | Setagaya ward | DT05 | 桜新町 | 世田谷区 |
| Sakuradai | SEIBU | Ikebukuro line | Nerima ward | SI05 | 桜台 | 練馬区 |
| Sakuradamon | Tokyo Metro | Yurakucho line | Chiyoda ward | Y-17 | 桜田門 | 千代田区 |
| Sakuragaoka | ODAKYU | Enoshima line | Kanagawa pref. | 桜ヶ丘 | 神奈川県 | |
| Sakuragicho | JR East | Negishi line | Kanagawa pref. | 桜木町 | 神奈川県 | |
| Sakuranbo-higashine | JR East | Yamagata shinkansen | Yamagata pref. | さくらんぼ東根 | 山形県 | |
| Samezu | KEIKYU | Honsen line | Shinagawa ward | KK05 | 鮫洲 | 品川区 |
| Sangen-jaya | TOKYU | Denen-toshi line | Setagaya ward | DT03 | 三軒茶屋 | 世田谷区 |
| Sangen-jaya | TOKYU | Setagaya line | Setagaya ward | SG01 | 三軒茶屋 | 世田谷区 |
| Sangubashi | ODAKYU | Odawara line | Shibuya ward | 参宮橋 | 渋谷区 | |
| Sasazuka | KEIO | Shinsen line | Shibuya ward | KO04 | 笹塚 | 渋谷区 |
| Sasazuka | KEIO | Keio line | Shibuya ward | KO04 | 笹塚 | 渋谷区 |
| Sashiogi | JR East | Kawagoe line | Saitama pref. | 指扇 | 埼玉県 | |
| Satsukidai | ODAKYU | Tama line | Kanagawa pref. | 五月台 | 神奈川県 | |
| Sawai | JR East | Ome line | Tokyo pref. | 沢井 | 東京都 | |
| Sayama-shi | SEIBU | Seibu-shinjuku line | Saitama pref. | SS26 | 狭山市 | 埼玉県 |
| Sayamagaoka | SEIBU | Ikebukuro line | Saitama pref. | SI20 | 狭山ヶ丘 | 埼玉県 |
| Seibi-jo | Tokyo Monorail | Tokyo Monorail line | Ota ward | 整備場 | 大田区 | |
| Seibu-chichibu | SEIBU | Seibu-chichibu line | Saitama pref. | SI36 | 西武秩父 | 埼玉県 |
| Seibu-kyujo-mae | SEIBU | Sayama line | Saitama pref. | SI41 | 西武球場前 | 埼玉県 |
| Seibu-kyujo-mae | SEIBU | Yamaguchi line | Tokyo pref. | SY03 | 西武球場前 | 東京都 |
| Seibu-shinjuku | SEIBU | Seibu-shinjuku line | Shinjuku ward | SS01 | 西武新宿 | 新宿区 |
| Seibu-tachikawa | SEIBU | Haijima line | Tokyo pref. | SS35 | 西武立川 | 東京都 |
| Seibu-yagisawa | SEIBU | Seibu-shinjuku line | Tokyo pref. | SS16 | 西武柳沢 | 東京都 |
| Seibu-yuenchi | SEIBU | Tamako line | Tokyo pref. | ST07 | 西武遊園地 | 東京都 |
| Seibu-yuenchi | SEIBU | Yamaguchi line | Tokyo pref. | SY01 | 西武遊園地 | 東京都 |
| Seibuen | SEIBU | Seibuen line | Tokyo pref. | SK06 | 西武園 | 東京都 |
| Seijyo-gakuen-mae | ODAKYU | Odawara line | Setagaya ward | 成城学園前 | 世田谷区 | |
| Seiseki-sakuragaoka | KEIO | Keio line | Tokyo pref. | KO27 | 聖跡桜ヶ丘 | 東京都 |
| Sendagaya | JR East | Sobu-chuo line | Shinjuku ward | 千駄ヶ谷 | 新宿区 | |
| Sendagi | Tokyo Metro | Chiyoda line | Bunkyo ward | C-15 | 千駄木 | 文京区 |
| Sendai | JR Kyushu | Kyushu shinkansen | Kagoshima pref. | 川内 | 鹿児島県 | |
| Sendai | JR East | Tohoku shinkansen | Miyagi pref. | 仙台 | 宮城県 | |
| Sengakuji | TOEI | Asakusa line | Minato ward | A-07 | 泉岳寺 | 港区 |
| Sengakuji | KEIKYU | Honsen line | Minato ward | A-07 | 泉岳寺 | 港区 |
| Sengawa | KEIO | Keio line | Tokyo pref. | KO13 | 仙川 | 東京都 |
| Sengendai | TOBU | Isesaki line/Skytree line | Saitama pref. | TS-24 | せんげん台 | 埼玉県 |
| Sengoku | TOEI | Mita line | Bunkyo ward | I-14 | 千石 | 文京区 |
| Senjyu-ohashi | KEISEI | Honsen line | Adachi ward | KS05 | 千住大橋 | 足立区 |
| Senkawa | Tokyo Metro | Fukutoshin line | Toshima ward | F-07 | 千川 | 豊島区 |
| Senkawa | Tokyo Metro | Yurakucho line | Toshima ward | Y-07 | 千川 | 豊島区 |
| Senzoku | TOKYU | Meguro line | Meguro ward | MG05 | 洗足 | 目黒区 |
| Senzoku-ike | TOKYU | Ikegami line | Ota ward | IK07 | 洗足池 | 大田区 |
| Serada | TOBU | Isesaki line | Gunma pref. | TI-21 | 世良田 | 群馬県 |
| Setagaya | TOKYU | Setagaya line | Setagaya ward | SG05 | 世田谷 | 世田谷区 |
| Setagaya-daita | ODAKYU | Odawara line | Setagaya ward | 世田谷代田 | 世田谷区 | |
| Shakujii-koen | SEIBU | Ikebukuro line | Nerima ward | SI10 | 石神井公園 | 練馬区 |
| Shiba-koen | TOEI | Mita line | Minato ward | I-05 | 芝公園 | 港区 |
| Shibamata | KEISEI | Kanamachi line | Katsushika ward | KS50 | 柴又 | 葛飾区 |
| Shibasaki | KEIO | Keio line | Tokyo pref. | KO15 | 柴崎 | 東京都 |
| Shibaura-futo | Yurikamome | Yurikamome line | Minato ward | U-05 | 芝浦ふ頭 | 港区 |
| Shibayama-chiyoda | KEISEI | Shibayama Railways | Chiba pref. | SR01 | 芝山千代田 | 千葉県 |
| Shibusawa | ODAKYU | Odawara line | Kanagawa pref. | 渋沢 | 神奈川県 | |
| Shibuya | JR East | Yamanote line | Shibuya ward | 渋谷 | 渋谷区 | |
| Shibuya | JR East | Saikyo line | Shibuya ward | 渋谷 | 渋谷区 | |
| Shibuya | JR East | Shonan-shinjuku line | Shibuya ward | 渋谷 | 渋谷区 | |
| Shibuya | Tokyo Metro | Fukutoshin line | Shibuya ward | F-16 | 渋谷 | 渋谷区 |
| Shibuya | Tokyo Metro | Ginza line | Shibuya ward | G-01 | 渋谷 | 渋谷区 |
| Shibuya | Tokyo Metro | Hanzomon line | Shibuya ward | Z-01 | 渋谷 | 渋谷区 |
| Shibuya | KEIO | Inokashira line | Shibuya ward | IN01 | 渋谷 | 渋谷区 |
| Shibuya | TOKYU | Toyoko line | Shibuya ward | TY01 | 渋谷 | 渋谷区 |
| Shibuya | TOKYU | Denen-toshi line | Shibuya ward | DT01 | 渋谷 | 渋谷区 |
| Shichinohe-towada | JR East | Tohoku shinkansen | Aomori pref. | 七戸十和田 | 青森県 | |
| Shiinamachi | SEIBU | Ikebukuro line | Toshima ward | SI02 | 椎名町 | 豊島区 |
| Shijyo-mae | Yurikamome | Yurikamome line | Koto ward | U-14 | 市場前 | 江東区 |
| Shiki | TOBU | Tojo line | Saitama pref. | TJ-14 | 志木 | 埼玉県 |
| Shimo | Tokyo Metro | Nanboku line | Kita ward | N-18 | 志茂 | 北区 |
| Shimo-akatsuka | TOBU | Tojo line | Itabashi ward | TJ-09 | 下赤塚 | 板橋区 |
| Shimo-igusa | SEIBU | Seibu-shinjuku line | Suginami ward | SS10 | 下井草 | 杉並区 |
| Shimo-itabashi | TOBU | Tojo line | Toshima ward | TJ-03 | 下板橋 | 豊島区 |
| Shimo-kitazawa | KEIO | Inokashira line | Setagaya ward | IN05 | 下北沢 | 世田谷区 |
| Shimo-kitazawa | ODAKYU | Odawara line | Setagaya ward | 下北沢 | 世田谷区 | |
| Shimo-maruko | TOKYU | Tokyu-tamagawa line | Ota ward | TM04 | 下丸子 | 大田区 |
| Shimo-ochiai | SEIBU | Seibu-shinjuku line | Shinjuku ward | SS03 | 下落合 | 新宿区 |
| Shimo-shinmei | TOKYU | Oimachi line | Shinagawa ward | OM02 | 下神明 | 品川区 |
| Shimo-takaido | KEIO | Keio line | Setagaya ward | KO07 | 下高井戸 | 世田谷区 |
| Shimo-takaido | TOKYU | Setagaya line | Setagaya ward | SG10 | 下高井戸 | 世田谷区 |
| Shimo-yamaguchi | SEIBU | Sayama line | Saitama pref. | SI40 | 下山口 | 埼玉県 |
| Shimousa-nakayama | JR East | Sobu-chuo line | Chiba pref. | 下総中山 | 千葉県 | |
| Shimura-sakaue | TOEI | Mita line | Itabashi ward | I-21 | 志村坂上 | 板橋区 |
| Shimura-sanchome | TOEI | Mita line | Itabashi ward | I-22 | 志村三丁目 | 板橋区 |
| Shin-akitsu | JR East | Musashino line | Tokyo pref. | 新秋津 | 東京都 | |
| Shin-aomori | JR East | Tohoku shinkansen | Aomori pref. | 新青森 | 青森県 | |
| Shin-aomori | JR Hokkaido | Hokkaido shinkansen | Aomori pref. | 新青森 | 青森県 | |
| Shin-banba | KEIKYU | Honsen line | Shinagawa ward | KK03 | 新馬場 | 品川区 |
| Shin-chiba | KEISEI | Chiba line | Chiba pref. | KS58 | 新千葉 | 千葉県 |
| Shin-daita | KEIO | Inokashira line | Setagaya ward | IN06 | 新代田 | 世田谷区 |
| Shin-egota | TOEI | Oedo line | Nerima ward | E-34 | 新江古田 | 練馬区 |
| Shin-fuji | JR Central | Tokaido shinkansen | Shizuoka pref. | 新富士 | 静岡県 | |
| Shin-hakodate-hokuto | JR Hokkaido | Hokkaido shinkansen | Hokkaido | 新函館北斗 | 北海道 | |
| Shin-hanamaki | JR East | Tohoku shinkansen | Iwate pref. | 新花巻 | 岩手県 | |
| Shin-isesaki | TOBU | Isesaki line | Gunma pref. | TI-24 | 新伊勢崎 | 群馬県 |
| Shin-itabashi | TOEI | Mita line | Itabashi ward | I-17 | 新板橋 | 板橋区 |
| Shin-iwakuni | JR West | Sanyo shinkansen | Yamaguchi pref. | 新岩国 | 山口県 | |
| Shin-kamagaya | HOKUSO/KEISEI | Hokuso/Narita Sky access line | Chiba pref. | HS08 | 新鎌ケ谷 | 千葉県 |
| Shin-kawasaki | JR East | Yokosuka line | Kanagawa pref. | 新川崎 | 神奈川県 | |
| Shin-kawasaki | JR East | Shonan-shinjuku line | Kanagawa pref. | 新川崎 | 神奈川県 | |
| Shin-kemigawa | JR East | Sobu-chuo line | Chiba pref. | 新検見川 | 千葉県 | |
| Shin-kiba | JR East | Keiyo line | Koto ward | 新木場 | 江東区 | |
| Shin-kiba | Tokyo Metro | Yurakucho line | Koto ward | Y-24 | 新木場 | 江東区 |
| Shin-kiba | TWR | Rinkai line | Koto ward | 新木場 | 江東区 | |
| Shin-kobe | JR West | Sanyo shinkansen | Hyogo pref. | 新神戸 | 兵庫県 | |
| Shin-kodaira | JR East | Musashino line | Tokyo pref. | 新小平 | 東京都 | |
| Shin-koenji | Tokyo Metro | Marunouchi line | Suginami ward | M-03 | 新高円寺 | 杉並区 |
| Shin-koganei | SEIBU | Tamagawa line | Tokyo pref. | SW02 | 新小金井 | 東京都 |
| Shin-koiwa | JR East | Sobu-chuo line | Katsushika ward | 新小岩 | 葛飾区 | |
| Shin-koiwa | JR East | Sobu line | Katsushika ward | 新小岩 | 葛飾区 | |
| Shin-koshigaya | TOBU | Isesaki line/Skytree line | Saitama pref. | TS-20 | 新越谷 | 埼玉県 |
| Shin-koshinzuka | TOEI | Arakawa line | Toshima ward | 新庚申塚 | 豊島区 | |
| Shin-koyasu | JR East | Keihin-tohoku line | Kanagawa pref. | 新子安 | 神奈川県 | |
| Shin-kurashiki | JR West | Sanyo shinkansen | Okayama pref. | 新倉敷 | 岡山県 | |
| Shin-maruko | TOKYU | Toyoko line | Kanagawa pref. | TY10 | 新丸子 | 神奈川県 |
| Shin-maruko | TOKYU | Meguro line | Kanagawa pref. | MG10 | 新丸子 | 神奈川県 |
| Shin-matsuda | ODAKYU | Odawara line | Kanagawa pref. | 新松田 | 神奈川県 | |
| Shin-matsudo | JR East | Joban line | Chiba pref. | 新松戸 | 千葉県 | |
| Shin-matsudo | JR East | Musashino line | Chiba pref. | 新松戸 | 千葉県 | |
| Shin-mikawashima | KEISEI | Honsen line | Arakawa ward | KS03 | 新三河島 | 荒川区 |
| Shin-minamata | JR Kyushu | Kyushu shinkansen | Kumamoto pref. | 新水俣 | 熊本県 | |
| Shin-misato | JR East | Musashino line | Saitama pref. | 新三郷 | 埼玉県 | |
| Shin-mobara | JR East | Sotobo line | Chiba pref. | 新茂原 | 千葉県 | |
| Shin-nakano | Tokyo Metro | Marunouchi line | Nakano ward | M-05 | 新中野 | 中野区 |
| Shin-narashino | JR East | Keiyo line | Chiba pref. | 新習志野 | 千葉県 | |
| Shin-nihonbashi | JR East | Sobu line | Chuo ward | 新日本橋 | 中央区 | |
| Shin-ochanomizu | Tokyo Metro | Chiyoda line | Chiyoda ward | C-12 | 新御茶ノ水 | 千代田区 |
| Shin-okachimachi | TOEI | Oedo line | Taito ward | E-10 | 新御徒町 | 台東区 |
| Shin-okachimachi | Tsukuba Express | Tsukuba Express line | Taito ward | 02 | 新御徒町 | 台東区 |
| Shin-okubo | JR East | Yamanote line | Shinjuku ward | 新大久保 | 新宿区 | |
| Shin-omuta | JR Kyushu | Kyushu shinkansen | Fukuoka pref. | 新大牟田 | 福岡県 | |
| Shin-onomichi | JR West | Sanyo shinkansen | Hiroshima pref. | 新尾道 | 広島県 | |
| Shin-osaka | JR Central | Tokaido shinkansen | Osaka pref. | 新大阪 | 大阪府 | |
| Shin-osaka | JR West | Sanyo shinkansen | Osaka pref. | 新大阪 | 大阪府 | |
| Shin-otsu | KEIKYU | Kurihama line | Kanagawa pref. | KK65 | 新大津 | 神奈川県 |
| Shin-otsuka | Tokyo Metro | Marunouchi line | Bunkyo ward | M-24 | 新大塚 | 文京区 |
| Shin-sakuradai | SEIBU | Seibu-yurakucho line | Nerima ward | SI38 | 新桜台 | 練馬区 |
| Shin-sayama | SEIBU | Seibu-shinjuku line | Saitama pref. | SS27 | 新狭山 | 埼玉県 |
| Shin-seibi-jo | Tokyo Monorail | Tokyo Monorail line | Ota ward | 新整備場 | 大田区 | |
| Shin-shibamata | HOKUSO | Hokuso line | Katsushika ward | HS01 | 新柴又 | 葛飾区 |
| Shin-shimonoseki | JR West | Sanyo shinkansen | Yamaguchi pref. | 新下関 | 山口県 | |
| Shin-shirakawa | JR East | Tohoku shinkansen | Fukushima pref. | 新白河 | 福島県 | |
| Shin-shiraoka | JR East | Tohoku line/Utsunomiya line | Saitama pref. | 新白岡 | 埼玉県 | |
| Shin-sugita | JR East | Negishi line | Kanagawa pref. | 新杉田 | 神奈川県 | |
| Shin-takashima | Minato-mirai | Minato-mirai line | Kanagawa pref. | MM02 | 新高島 | 神奈川県 |
| Shin-takashimadaira | TOEI | Mita line | Itabashi ward | I-26 | 新高島平 | 板橋区 |
| Shin-tamana | JR Kyushu | Kyushu shinkansen | Kumamoto pref. | 新玉名 | 熊本県 | |
| Shin-tokorozawa | SEIBU | Seibu-shinjuku line | Saitama pref. | SS24 | 新所沢 | 埼玉県 |
| Shin-tosu | JR Kyushu | Kyushu shinkansen | Fukuoka pref. | 新鳥栖 | 福岡県 | |
| Shin-toyosu | Yurikamome | Yurikamome line | Koto ward | U-15 | 新豊洲 | 江東区 |
| Shin-urayasu | JR East | Keiyo line | Chiba pref. | 新浦安 | 千葉県 | |
| Shin-yahashira | JR East | Musashino line | Chiba pref. | 新矢柱 | 千葉県 | |
| Shin-yamaguchi | JR West | Sanyo shinkansen | Yamaguchi pref. | 新山口 | 山口県 | |
| Shin-yatsushiro | JR Kyushu | Kyushu shinkansen | Kumamoto pref. | 新八代 | 熊本県 | |
| Shin-yokohama | JR Central | Tokaido shinkansen | Kanagawa pref. | 新横浜 | 神奈川県 | |
| Shin-yurigaoka | ODAKYU | Odawara line | Kanagawa pref. | 新百合ヶ丘 | 神奈川県 | |
| Shin-yurigaoka | ODAKYU | Tama line | Kanagawa pref. | 新百合ヶ丘 | 神奈川県 | |
| Shinagawa | JR East | Yamanote line | Minato ward | 品川 | 港区 | |
| Shinagawa | JR East | Keihin-tohoku line | Minato ward | 品川 | 港区 | |
| Shinagawa | JR East | Tokaido line | Minato ward | 品川 | 港区 | |
| Shinagawa | JR East | Yokosuka line | Minato ward | 品川 | 港区 | |
| Shinagawa | JR Central | Tokaido shinkansen | Minato ward | 品川 | 港区 | |
| Shinagawa | KEIKYU | Honsen line | Minato ward | KK01 | 品川 | 港区 |
| Shinagawa-seaside | TWR | Rinkai line | Shinagawa ward | 品川シーサイド | 品川区 | |
| Shinanomachi | JR East | Sobu-chuo line | Shinjuku ward | 信濃町 | 新宿区 | |
| Shinbashi | JR East | Yamanote line | Minato ward | 新橋 | 港区 | |
| Shinbashi | JR East | Keihin-tohoku line | Minato ward | 新橋 | 港区 | |
| Shinbashi | JR East | Tokaido line | Minato ward | 新橋 | 港区 | |
| Shinbashi | JR East | Yokosuka line | Minato ward | 新橋 | 港区 | |
| Shinbashi | TOEI | Asakusa line | Minato ward | A-10 | 新橋 | 港区 |
| Shinbashi | Tokyo Metro | Ginza line | Minato ward | G-08 | 新橋 | 港区 |
| Shinbashi | Yurikamome | Yurikamome line | Minato ward | U-01 | 新橋 | 港区 |
| Shinden | TOBU | Isesaki line/Skytree line | Saitama pref. | TS-18 | 新田 | 埼玉県 |
| Shingashi | TOBU | Tojo line | Saitama pref. | TJ-20 | 新河岸 | 埼玉県 |
| Shinjo | JR East | Yamagata shinkansen | Yamagata pref. | 新庄 | 山形県 | |
| Shinjuku | JR East | Yamanote line | Shinjuku ward | 新宿 | 新宿区 | |
| Shinjuku | JR East | Sobu-chuo line | Shinjuku ward | 新宿 | 新宿区 | |
| Shinjuku | JR East | Saikyo line | Shinjuku ward | 新宿 | 新宿区 | |
| Shinjuku | JR East | Chuo line | Shinjuku ward | 新宿 | 新宿区 | |
| Shinjuku | JR East | Shonan-shinjuku line | Shinjuku ward | 新宿 | 新宿区 | |
| Shinjuku | TOEI | Oedo line | Shibuya ward | E-27 | 新宿 | 渋谷区 |
| Shinjuku | TOEI | Shinjuku line | Shinjuku ward | S-01 | 新宿 | 新宿区 |
| Shinjuku | Tokyo Metro | Marunouchi line | Shinjuku ward | M-08 | 新宿 | 新宿区 |
| Shinjuku | KEIO | Keio line | Shinjuku ward | KO01 | 新宿 | 新宿区 |
| Shinjuku | ODAKYU | Odawara line | Shinjuku ward | 新宿 | 新宿区 | |
| Shinjuku-gyoenmae | Tokyo Metro | Marunouchi line | Shinjuku ward | M-10 | 新宿御苑前 | 新宿区 |
| Shinjuku-nishiguchi | TOEI | Oedo line | Shinjuku ward | E-01 | 新宿西口 | 新宿区 |
| Shinjuku-sanchome | TOEI | Shinjuku line | Shinjuku ward | S-02 | 新宿三丁目 | 新宿区 |
| Shinjuku-sanchome | Tokyo Metro | Fukutoshin line | Shinjuku ward | F-13 | 新宿三丁目 | 新宿区 |
| Shinjuku-sanchome | Tokyo Metro | Marunouchi line | Shinjuku ward | M-09 | 新宿三丁目 | 新宿区 |
| Shinmachi | JR East | Takasaki line | Gunma pref. | 新町 | 群馬県 | |
| Shinonome | TWR | Rinkai line | Koto ward | 東雲 | 江東区 | |
| Shinozaki | TOEI | Shinjuku line | Edogawa ward | S-20 | 篠崎 | 江戸川区 |
| Shinrin-koen | TOBU | Tojo line | Saitama pref. | TJ-30 | 森林公園 | 埼玉県 |
| Shinsen | KEIO | Inokashira line | Shibuya ward | IN02 | 神泉 | 渋谷区 |
| Shinsen-shinjuku | KEIO | Shinsen line | Shinjuku ward | KO01 | 新線新宿 | 新宿区 |
| Shintomicho | Tokyo Metro | Yurakucho line | Chuo ward | Y-20 | 新富町 | 中央区 |
| Shiodome | TOEI | Oedo line | Minato ward | E-19 | 汐留 | 港区 |
| Shiodome | Yurikamome | Yurikamome line | Minato ward | U-02 | 汐留 | 港区 |
| Shioiri | KEIKYU | Honsen line | Kanagawa pref. | KK58 | 汐入 | 神奈川県 |
| Shiomi | JR East | Keiyo line | Koto ward | 潮見 | 江東区 | |
| Shiraitodai | SEIBU | Tamagawa line | Tokyo pref. | SW04 | 白糸台 | 東京都 |
| Shiraoka | JR East | Tohoku line/Utsunomiya line | Saitama pref. | 白岡 | 埼玉県 | |
| Shiroi | HOKUSO | Hokuso line | Chiba pref. | HS10 | 白井 | 千葉県 |
| Shiroishi-zao | JR East | Tohoku shinkansen | Miyagi pref. | 白石蔵王 | 宮城県 | |
| Shirokane-dai | TOEI | Mita line | Minato ward | I-02 | 白金台 | 港区 |
| Shirokane-dai | Tokyo Metro | Nanboku line | Minato ward | N-02 | 白金台 | 港区 |
| Shirokane-takanawa | TOEI | Mita line | Minato ward | I-03 | 白金高輪 | 港区 |
| Shirokane-takanawa | Tokyo Metro | Nanboku line | Minato ward | N-03 | 白金高輪 | 港区 |
| Shiromaru | JR East | Ome line | Tokyo pref. | 白丸 | 東京都 | |
| Shisui | JR East | Narita line | Chiba pref. | 酒々井 | 千葉県 | |
| Shizu | KEISEI | Honsen line | Chiba pref. | KS32 | 志津 | 千葉県 |
| Shizukuishi | JR East | Akita shinkansen | Iwate pref. | 雫石 | 岩手県 | |
| Shizuoka | JR Central | Tokaido shinkansen | Shizuoka pref. | 静岡 | 静岡県 | |
| Shoinjinja-mae | TOKYU | Setagaya line | Setagaya ward | SG04 | 松陰神社前 | 世田谷区 |
| Shomaru | SEIBU | Seibu-chichibu line | Saitama pref. | SI33 | 正丸 | 埼玉県 |
| Shonandai | ODAKYU | Enoshima line | Kanagawa pref. | 湘南台 | 神奈川県 | |
| Showajima | Tokyo Monorail | Tokyo Monorail line | Ota ward | 昭和島 | 大田区 | |
| Sobudai-mae | ODAKYU | Odawara line | Kanagawa pref. | 相武台前 | 神奈川県 | |
| Sodegaura | JR East | Uchibo line | Chiba pref. | 袖ヶ浦 | 千葉県 | |
| Soga | JR East | Keiyo line | Chiba pref. | 蘇我 | 千葉県 | |
| Soga | JR East | Sotobo line | Chiba pref. | 蘇我 | 千葉県 | |
| Soga | JR East | Uchibo line | Chiba pref. | 蘇我 | 千葉県 | |
| Sogo-sando | KEISEI | Honsen line | Chiba pref. | KS38 | 宗吾参道 | 千葉県 |
| Soka | TOBU | Isesaki line/Skytree line | Saitama pref. | TS-16 | 草加 | 埼玉県 |
| Soshigaya-okura | ODAKYU | Odawara line | Setagaya ward | 祖師ヶ谷大蔵 | 世田谷区 | |
| Suehirocho | Tokyo Metro | Ginza line | Chiyoda ward | G-14 | 末広町 | 千代田区 |
| Sugamo | JR East | Yamanote line | Toshima ward | 巣鴨 | 豊島区 | |
| Sugamo | TOEI | Mita line | Toshima ward | I-15 | 巣鴨 | 豊島区 |
| Sugamo-shinden | TOEI | Arakawa line | Toshima ward | 巣鴨新田 | 豊島区 | |
| Sugano | KEISEI | Honsen line | Chiba pref. | KS15 | 菅野 | 千葉県 |
| Sugita | KEIKYU | Honsen line | Kanagawa pref. | KK46 | 杉田 | 神奈川県 |
| Suidobashi | JR East | Sobu-chuo line | Chiyoda ward | 水道橋 | 千代田区 | |
| Suidobashi | TOEI | Mita line | Bunkyo ward | I-11 | 水道橋 | 文京区 |
| Suitengu-mae | Tokyo Metro | Hanzomon line | Chuo ward | Z-10 | 水天宮前 | 中央区 |
| Sumiyoshi | TOEI | Shinjuku line | Koto ward | S-13 | 住吉 | 江東区 |
| Sumiyoshi | Tokyo Metro | Hanzomon line | Koto ward | Z-12 | 住吉 | 江東区 |
| Suzukakedai | TOKYU | Denen-toshi line | Tokyo pref. | DT24 | すずかけ台 | 東京都 |
| Suzukicho | KEIKYU | Daishi line | Kanagawa pref. | KK22 | 鈴木町 | 神奈川県 |
| Suzumenomiya | JR East | Tohoku line/Utsunomiya line | Tochigi pref. | 雀宮 | 栃木県 |