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

In 1961, the integration of courses B I and B II into the Didactic section of the Pedagogic Faculty took place. Due to differences in curriculum, the Didactic Section became Didactic Section I, while the former B I and B II courses became Didactic Section II. In further developments, based on the Decree of the Minister of P and K Number 92 of 1962, an educational institution was established under the name of the Teacher Education Institute (IPG). 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 3rd, 1963, stipulated the unification of FKIP and IPG to become the Teaching and Education Institute (IKIP).

As a follow-up to the Presidential Decree, the Decree of the Minister of PTIP was issued No. 55 of 1963, dated May 22nd, 1963 concerning the establishment of IKIP Jakarta, IKIP Bandung, IKIP Yogyakarta, and IKIP Malang since May 1st, 1963. IKIP Yogyakarta was inaugurated by the Minister of PTIP on May 21st, 1964 This date was designated as the Anniversary of IKIP Yogyakarta.

In the early days of his birth, September 21st,1964 through September 1st, 1965, IKIP Yogyakarta was led by a presidium. Based on the Chancellor's Decree No. 05 of 1965, the organizational structure of IKIP Yogyakarta states that there is a Teacher Training Faculty of Exata Sciences (FKIE) with its majors: Life Sciences, Natural Sciences, Chemistry and Definitive Sciences.

Based on the Decree of the President of the Republic of Indonesia Number 54 of 1982, September 7, 1982 there was a change in the organizational structure of the Yogyakarta Teachers' Training College, including changing the name of FKIE to the Faculty of Mathematics and Natural Science Education (FPMIPA). Furthermore, the Minister of Education and Culture through Decree Number 0554/0/1983 dated December 8th, 1983 stipulated in detail the type and number of departments in the faculties within the IKIP Yogyakarta. 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 with Number 31/DIKTI/Kep/1984 dated May 17th, 1984 stipulated in detail the type and number of study programs in each department at the faculties of IKIP Yogyakarta. The Department of Physics Education organizes the Physics Education study program.

In 1997, the Physics Education Department opened a new study program for the 1997/1998 school year, namely the Physics Study Program based on the Letter of the Director General of Higher Education No. 1259/DT/T/97, dated May 29th, 1997 concerning permission to open non-educational study programs at FPMIPA IKIP Yogyakarta. Furthermore, with the Decree of the President of the Republic of Indonesia Number 93 of 1999 dated August 31, 1999 concerning the change in Status from the Yogyakarta Teachers' Training College to the Yogyakarta State University (UNY), FPMIPA changed to the Faculty of Mathematics and Natural Sciences (FMIPA) and the Physics Education Department officially had a Physics study program.