Based on Government Regulation No. 37 of 1950, Gadjah Mada University (UGM) opened the Faculty of Literature in Pedagogic and Philosophy. On September 19, 1950, the faculty was divided into three faculties, namely: Literature and Culture, Pedagogic, General and Philosophy. During the period December 1950 to September 1958 in Yogyakarta, courses B I and B II were opened for several majors. In the mid 1960s, the Faculty of Pedagogic UGM opened the Didactic Section, which included the Department of Natural Sciences.

In 1961, the integration of B I and B II courses into the Didactic section of the Pedagogic Faculty. Due to differences in curriculum, the Didactic Section becomes part Didactic I, while the former courses B I and B II become part Didactic II. In further development, based on the decision of the Minister of Education and Culture No. 92/1962, an educational institution called the Institute of Teacher Education (IPG) was established. Meanwhile, FIP, FPD, and FKIP are still faculties at Gadjah Mada University, under the supervision of the PTIP Department. To overcome this dualism, Presidential Decree No. 1 of 1963, dated January 3, 1963, issued the unification of FKIP and IPG into the Institute of Teacher Training and Education (IKIP).

As a follow up to the Presidential Decree, the Decree of the Minister of PTIP No. 55 of 1963 was issued, on May 22, 1963 concerning the establishment of IKIP Jakarta, IKIP Bandung, IKIP Yogyakarta, and IKIP Malang since May 1, 1963. IKIP Yogyakarta was established by the Minister of PTIP on May 21, 1964 The date was set as IKIP Yogyakarta Anniversary.

In the early days of his birth, 21 September 1964 s.d. September 1, 1965, IKIP Yogyakarta was led by a presidium. Based on the Chancellor's Decree No. 05 of 1965, the structure of the IKIP Yogyakarta organization mentioned the existence of the Faculty of Teacher Training in Exata Science (FKIE) with its majors: Life Sciences, Natural Sciences, Chemistry and Definite Sciences.

Based on the Republic of Indonesia's Presidential Decree Number 54 of 1982, on September 7, 1982 there was a change in the organizational structure of IKIP Yogyakarta, including the change in the name of FKIE to the Faculty of Mathematics and Natural Sciences (FPMIPA). Furthermore, the Minister of Education and Culture through Decree Number 0554/0/1983 dated December 8, 1983 established in detail the type and number of majors in faculties within the IKIP Yogyakarta environment. FPMIPA has four majors, namely: Mathematics Education, Physics Education, Chemistry Education and Biology Education. The Director General of Higher Education Ministry of Education and Culture No. 31 / DIKTI / Kep / 1984 dated May 17, 1984 stipulates in detail the type and number of study programs in each department at the faculties of IKIP Yogyakarta. The Physics Education Department organizes Physics Education study programs.

Science Education Program - Faculty of Mathematics and Natural Sciences Yogyakarta State University was established on December 21, 2006 according to the Decree of the Director General of Higher Education No. 4906 / D / T / 2006. At present the Science Study Program of Natural Sciences FMIPA UNY obtains accreditation B from BAN PT.

Starting in 2014 the Natural Sciences Education Study Program has implemented a new curriculum that refers to the National College Standards (SNPT) and the Indonesian National Qualification Framework (KKNI) so that graduates of the Natural Sciences Education Study Program are expected to be able to compete at the national and international levels.