Based on Government Regulation Number 37 of 1950, Gadjah Mada University (UGM) opened the Faculty of Pedagogical Literature and Philosophy. On September 19 1950, the faculty was split into three faculties, namely: Literature and Culture, Pedagogics, General Affairs and Philosophy. In the period from December 1950 to September 1958 in Yogyakarta, B I and B II courses were opened for several majors. In the mid-1960s, the UGM Faculty of Pedagogy opened a Didactics Section, one of its departments being the Department of Natural Sciences.

In 1961, there was an integration of the B I and B II courses into the Didactic section of the Pedagogical Faculty. Due to differences in curriculum, the Didactic Section became Didactic Section I, while the former courses B I and B II became Didactic Section II. In subsequent developments, based on Ministerial Decree Number 92 of 1962, an educational institution was established with the name Institute of Teacher Education (IPG). Meanwhile, FIP, FPD, and FKIP are still faculties at Gadjah Mada University, under the supervision of the PTIP Department. To overcome this dualism, Republic of Indonesia Presidential Decree Number 1 of 1963, January 3 1963, stipulated the unification of FKIP and IPG to become the Teacher Training and Education Institute (IKIP).

As a follow-up to the Presidential Decree, PTIP Ministerial Decree Number 55 of 1963 was issued, dated 22 May 1963 concerning the establishment of IKIP Jakarta, IKIP Bandung, IKIP Yogyakarta, and IKIP Malang from 1 May 1963. IKIP Yogyakarta was inaugurated by the Minister of PTIP on 21 May 1964 . This date is set as the Anniversary of IKIP Yogyakarta.

In the early days of his birth, 21 September 1964 until. September 1 1965, IKIP Yogyakarta was led by a presidium. Based on Chancellor's Decree Number 05 of 1965, the organizational structure of IKIP Yogyakarta states that there is a Teachers' Faculty of Extrinsic Sciences (FKIE) with departments: Life Sciences, Natural Sciences, Chemical Sciences and Exact Sciences.

Based on Presidential Decree Number 54 of 1982, on 7 September 1982 there was a change in the organizational structure of IKIP Yogyakarta, including changing the name of FKIE to Faculty of Mathematics and Natural Sciences Education (FPMIPA). Furthermore, the Minister of Education and Culture through Decree Number 0554/0/1983 dated 8 December 1983 determined in detail the types and number of departments in the faculties within IKIP Yogyakarta. FPMIPA has four departments, namely: Mathematics Education, Physics Education, Chemistry Education and Biology Education. The Director General of Higher Education, Ministry of Education and Culture, Number 31/DIKTI/Kep/1984 dated 17 May 1984 determined in detail the types and number of study programs in each department at the faculty within IKIP Yogyakarta. The Physics Education Department organizes the Physics Education study program.

The Science Education Study Program- Faculty of Mathematics and Natural Sciences, Yogyakarta State University was established on December 21 2006 in accordance with the Decree of the Director General of Higher Education No 4906/D/T/2006. The history of the development of accreditation for the Science Education Study Program is as follows:

• July 1, 2011 to. 1 July 2016 Accreditation B by BAN PT with Accreditation Number 009/ BAN-PT/ AK-XIV/ S1/ VII/ 2011
• 10 June 2016 s.d. 10 June 2021 Accreditation A by BAN PT with Accreditation Number 0826/ SK/ BAN-PT/ Akred/ S/ VI/ 2016
• May 5, 2021 s.d. 30 September 2025 Superior Accreditation by BAN PT with Accreditation Number 2719/ SK/ BAN-PT/ Akred-Itnl/ S/ V/ 2021
• 20 March 2020 s.d. 30 September 2025 ASIIN International Accreditation

Currently, the Science Education Study Program applies the Independent Campus Learning Curriculum (MBKM) in accordance with the implementation of Minister of Education and Culture Regulation Number 3 of 2020 concerning National Higher Education Standards.