The implementation of the Postgraduate Program in Physics began with the establishment of the master's program which began to open in 1981 with Prof. Dr. Prayoto, M.Sc. as the manager and the first student as many as 3 people. Over time, it was felt necessary to develop by increasing the level of education that could be held, namely at the doctoral level.

Decree of the Higher Education Number 580 / Dikti / Kep /  1993 dated September 23, 1993, is a decree for the establishment of the Master's Program in Physical Sciences and a Doctoral Program in Mathematics and Natural Sciences Study Program. So the Doctor of Physical Sciences program is part of the doctoral in Mathematical Sciences and Natural Sciences.

Based on the Rector's Decree Number 89 / P / SK / HT / 2006 dated March 9, 2006, the Post-UGM Program is divided into 2 programs, namely Monodisciplinary and Multidisciplinary. The Doctoral Program in Physical Sciences includes a Monodisciplinary Study Program whose curriculum comes from one field of science organized and managed by the relevant Faculty. Starting from the 2006/2007 academic year, all management and administration are carried out by the Faculty of Mathematics and Natural Sciences.

The Physics Doctoral Study Program is held to help the government in developing education and research in the field of Physics. The implementation of the Physics Doctoral Study Program is supported by the existence of 4 laboratories under the management of the Department of Physics, namely the Atomic and Core Physics Laboratory, Fismatel, Geophysics, Basic Physics, and Laboratories managed by the Department of Physics FMIPA UGM and LPPT under the university. Supported by 35 lecturers, the Physics Doctoral Study Program manages and educates 50 students per year (student body).

Since 2021, the S3 Physics Study Program has changed its name to the Physics Doctoral Study Program. For quality assurance, the UGM Physics Doctoral Study Program is annually audited by the UGM Quality Assurance Office through Internal Quality Audit (AMI) and every 5 years is accredited by the National Accreditation Board for Higher Education (BAN-PT). Until 2022, the UGM Physics Doctoral Study Program has received an A accreditation rating.

Since the enactment of the Rector's Decree Number 18 of 2019 concerning the Implementation of Research-based Postgraduate (Master and Doctoral) Programs (Research), the Physics Doctoral Study Program FMIPA UGM has organized a research-based Doctoral program (by Research).