The now called GS YSU was first established in 1981. At that time, this unit, affiliated to IKIP Jakarta (Jakarta Institute of Teachers Training and Educational Sciences), offered only one master’s program, i.e. Educational Research and Evaluation. In the period of 1981-1986, Ford Foundation facilitated its development by providing an expert in educational research. In 1983, this unit started to offer Master’s Program in Technology and Vocational Education.

Ten years later or in 1993, Yogyakarta State University, formerly called IKIP Yogyakarta, obtained an independent authority to organize its own graduate programs under a decree number 432/DIKTI/Kep1993 issued on June 16, 1993 by Directorate General of Higher Education, Ministry of Education and Culture. This enabled the institution to establish three more study programs, i.e. Master’s Programs in Educational Management, Non-Formal Education, and Social Studies Education. By 2005, Graduate School YSU has managed to offer 14 study programs comprising both Master’s (S2) and Doctoral programs (S3).

In 2014, there are currently 34 programs offered. In the Doctoral level, the programs offered are Doctoral Programs in Educational Research and Evaluation, Educational Sciences, Vocational Education, Educational Administration, and Language Education Science. The Master’s Programs are Master’s Programs in Educational Research and Evaluation, Vocational Education, Educational Administration, Non-Formal Education, Social Studies Education, Applied Linguistics, Instructional Technology, Mathematics Education, Sports Science, Primary Education, Guidance & Counseling, Science Education, Javanese Language Education, Indonesian Language and Literature Education, English Language Education, Early Childhood Education, History Education, Economics Education, Electronics Technology and  Informatics Education, Electrical Engineering Education,  Mechanical Engineering Education,  Family Welfare Education, Art Education, Biology Education, Physics Education, Geography Education, Chemistry Education, Special Education, and Civic Education. All the study programs support various areas of interest.

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