The creation of the Department is connected with the start of the Faculty of Education activity in 1946, on which was established the Institute of Physics. In this period, the Department devoted its activity to the education of teachers of physics. A separate Department of physics was founded in 1954. The first Chair of the department became Prof. Dr. Josef Fuka.

In 1960, from the Department of Physics separated the Department of theoretical physics and astronomy headed by Prof. Dr. Bedřich Havelka, DrSc. and the name of the Department was changed to the Department of experimental physics and physics methodology. In 1962 was created the Department of optics and fine mechanics, headed by Prof. Dr. Engelbert Keprt.

In 1975 the structure of the Departments of Physics was rearranged and the two departments were established: the Department of physics and Didactics of physics and the Department of optics and fine mechanics. In 1975 the Department was headed by Prof. Dr. Josef Fuka and after him by Prof. Dr. Ivan Cabák, CSc.

Until 1978 the Department remained the only guarantor of the teaching of physics study program. In 1978 it became also a guarantor of a study program Biophysics and chemical physics. In accordance with this the Department was gradually transformed into two departments: Didactics of Physics and Didactic Techniques (since 1980) and Biophysics (since 1989).

In 1989, the Department's name was changed to its current one, and the Chair of the Department became Prof. Dr. Ing. Jaroslav Pospíšil, DrSc. In 1992 the Department became a guarantor of further programs of studies: Applied Physics with a focus on the instrumentation physics and metrology. From 1993, the Department was headed by Assoc. Prof. Dr. Vladislav Kolesnikov, CSc. From 1999 the Chair of the Department was doc. RNDr. Roman Kubínek, CSc. who was followed by Prof. RNDr. Miroslav Mašláň, CSc. Then the Department was headed again by doc. Roman Kubínek, CSc. Currently the Chair of the Department is doc. RNDr. Libor Machala, Ph.D.

In 2006 the Department didactics section joined a part of the staff from the canceled Department of Theoretical Physics. In the year 2011 from the Department separated the Biophysics section, which established a new Department, and at the same time there was a transfer of some personnel from the Centre for Research of Nanomaterials, the predecessor of the Regional Center of Advanced Technologies and Materials.

Since the year 2012 the Department has guaranteed a full-scope study in the field of Nanotechnology (Bachelor’s and Master's programs). In the years of 2015/2016 there were some changes in the staff of the Department due to a shift of its main focus on a scientific research in the area of nanotechnology and nuclear spectroscopic methods.