This is a list of single gender schools (boys' schools and girls' schools) in Japan.

• Hikarigaoka Girls' High School

• Wayo Konodai Girls' Junior High School & Senior High School [ja]

• Gifu Daiichi High School - Boys' school

• Sonoda Gakuen Junior High School & Senior High School [ja] - Amagasaki - Girls' school

Boys' schools

• Asano Junior & Senior High School
• Eiko Gakuen
• Keio Senior High School
• Keio Futsubu School a.k.a. Keio Gijuku Futsubu (慶應義塾普通部, Keiō Gijuku Futsubu; junior high school)

Girls schools

• Caritas Girls' Junior & Senior High School
• Ferris Girls' Junior & Senior High School (Yokohama)
• Hosei University Girls' High School
• Kamakura Jogakuin Junior and Senior High School
• Kanrei Shirayuri Gakuen Junior/Senior High School
• Kitakamakura Girls' High School
• Kanrei Shirayuri Gakuen Junior/Senior High School (Hakone)
• Seishin Girls' High School [ja]
• Shonan Joshi Senior High School
• Shonan Shirayuri Gakuen Junior High School and High School (Fujisawa)
• Takagi Gakuen Girls' High School
• Yokohama Eiri Girls' High School [ja]
• Yokohama International Girls' Institute Suiryo High School
• Yokohama Jogakuin Junior and Senior High School

• Kobe Kaisei Girls' Junior & Senior High School
• Kōbe Yamate Girls' Junior & Senior High School [ja]
• Kōbe Tokiwa Girls' High School [ja]

• Tamana Girls High School

• Sendai Shirayuri Gakuen Junior High School and High School

• Eifu Girls' Upper Secondary Specialized Training School [ja]
• Osaka Seikei Girls' High School
• Osaka Jogakuin Junior and Senior High School
• Osaka Kunei Jogakuin Junior and Senior High School [ja]
• Osaka Shin-Ai Jogakuin (Elementary through High School)
• Ohtani Junior and Senior High School
• Poole Gakuin Junior and Senior High School [ja]

• Keio Shiki Senior High School - Boys' school

• Seien Girls' High School (Hamamatsu)

Separate boys' and girls' schools

• Jiyu Gakuen [ja] - Coeducational for elementary school and separate gender for junior-senior high school

Boys' schools

• Azabu High School
• Gakushuin Boys' Junior and Senior High School [ja]
• Gyosei Junior and Senior High School
• Gyosei Primary School (暁星小学校)
• Kaisei Academy
• Kogyokusha Junior High and Senior High School [ja]
• Musashi Junior and Senior High School
• Rikkyo Ikebukuro Junior and Senior High School
• St. Mary's International School
• Seigakuin Junior & Senior High School
• Seisoku Gakuen Senior High School [ja]
• Takanawa Junior / Senior High School [ja]
• Tokyo Gakuen High School
• Waseda University Junior and Senior High School

Girls' schools

• Chiyoda Jo-Gakuen Junior and Senior High School [ja]
• Edogawa Girls' Junior & High School [ja]
• Fujimi Junior & Senior High School [ja]
• Fujimura Girls' Junior and Senior High School [ja]
• Futaba Gakuen Elementary School (雙葉小学校), girls' school
• Futaba Gakuen Junior and Senior High School [ja]
• Gakushuin Girls' Junior and Senior High School [ja] (Shinjuku)
• Hosen Gakuen Junior and Senior High School [ja] - Has coeducational and girls' only sections
• International School of the Sacred Heart (all girls' for grades 1-12)
• Joshigakuin Junior and Senior High School [ja]
• Joshi Seigakuin Junior & Senior High School
• Joshibi High School of Art and Design
• Juntoku Girls' High School [ja]
• Kanda Jo-Gakuen Junior and Senior High School [ja]
• Keio Girls Senior High School
• Kichijo Girls' School [ja] (junior and senior high school)
• Koka Gakuen Junior & Senior High School for Girls [ja]
• Komazawa Gakuen Girls' Junior High School-Senior High School [ja]
• Kunimoto Alberta International School
• Kunimoto Girls' Junior and Senior High School [ja]
• Kyōritsu Joshi Junior and Senior High School [ja], affiliated with Kyoritsu Women's University
• Miwada Gakuen Junior and Senior High School [ja]
• Nakamura Junior & Senior Girls' High School [ja]
• Nihon Ongaku High School [ja] (plans to become coeducational in 2023, with the new name Shinagawa Gakugei High School (品川学藝高等学校))^[1]
• Ohyu Gakuen Girls' Junior and Senior High School [ja]
• Ōtsuma Junior and Senior High School [ja], affiliated with Otsuma Women's University
• Otsuma Nakano Junior and Senior High School [ja]
• Otsuma Tama Junior and Senior High School [ja]
• St. Hilda's School (Kōran Jogakkō Junior High and Senior High School [ja])
• Sacred Heart School in Tokyo
• Seisen International School
• Shinagawa Etoile Girls' High School [ja]
• Shinagawa Joshi Gakuin Junior High and Senior High School [ja]
• Shirayuri Joshi Gakuen Elementary School (白百合学園小学校), girls' school, affiliated with Shirayuri Women's University
• Shirayuri Joshi Gakuen Junior and Senior High School [ja], affiliated with Shirayuri Women's University
• Shoei Girls' Junior and Senior High School
• Showa Women's University Junior-Senior High School
• Tachikawa Girls' High School [ja]
• Toho Girls' Junior and Senior High School [ja]
• Tokyo Joshi Gakuin Junior & Senior High School [ja] (junior and senior high school)
• Wayō Kudan Joshi Gakuen Junior and Senior High School [ja], affiliated with Wayo Women's University

Boys'

• Hachioji Academy (became coeducational in 1947)

Girls'

• Aoyama Gakuin Yokohama Eiwa High School (was a girls' school until 2018)
• Jiyu Gakuen Girls' School (Tokyo)
• Ono Gakuen Girls' Junior High and Senior High School (小野学園女子中学・高等学校), now Shinagawa Shouei Junior and Senior High School [ja]
• Osaka Girls' Senior High School, became coeducational and is now Abeno Shogaku High School
• Sagano Girls' High School, became coeducational in 1950 as Sagano High School