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 Tokyo Gakugei University was formally chartered as a university in 1949 when four teacher training institutions in Tokyo from the pre-war era were merged. These institutions (Tokyo First, Second, and Third Normal School and Tokyo Youth Normal School) in turn trace their history back to the Tokyo School of Training Elementary School Teachers founded in 1873 and Tokyo Women's Normal School founded in 1900.

 Ever since its founding, the university has sent its graduates in large numbers to serve as educators throughout Japan, developing into an institution with a fine tradition of teacher education.

 At the time the university was chartered, the main campuses were located in Setagaya, Koganei, Oizumi, Takehaya, and Oiwake, with a branch school in Chofu. The first two years of courses were taught on the Koganei, Oizumi, Takehaya, and Oiwake campuses, while the third and fourth years took place in Setagaya. The Chofu branch was abolished in 1951 as part of a consolidation plan. Eventually the other campuses were closed as well and all education took place at the present Koganei location starting in 1964.

 In 1966 the Faculty of Liberal Arts was changed to Faculty of Education, and a Graduate School of Education (master's program) was established to provide education and research in a wide range of fields from humanities and social sciences to natural science, physical education, and the arts, training capable educators equipped with a high level of specialized knowledge and skills.

 In 1973 a Department for Special Needs Education was established enabling the training of educators specializing in teaching persons with any of a wide range of physical or mental disabilities.

 In 1988 a Liberal Arts Division was added alongside the Teacher Training Division to develop educators capable of contributing to society in fields other than school education and with the intention of bringing up human resources meeting the needs of the age.

 In 1996 the United Graduate School of Education (doctoral course) was established jointly with Saitama University, Chiba University, and Yokohama National University as an interuniversity graduate school for the purpose of developing researchers mainly in the field of curriculum studies. Then in 1997 a Comprehensive Educational Development major was added to the master's program, made up exclusively of evening courses. Other evening courses were started thereafter aimed at people currently in the teaching profession, as well as a short-term special course lasting one year, as part of ongoing efforts to advance research in the field of education and to enhance programs for in-service teachers.

 In 2004, with changes in the nation's higher education policies, the university was incorporated and a national university and established its present administrative structure.

 In 2008 the Professional Degree Program (Graduate School of Teacher Education) was established in the Graduate School of Education as an effort to enhance the university's contribution to education in Japan.

 In 2015, the Teacher Training Division was reorganized as the School Education Division, and the Liberal Arts Division was reorganized as the Educational Specialist Division.

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