The Doctor of Philosophy in Engineering (Ph.D. in Engineering) degree is awarded to candidates who successfully complete the taught courses and research components of the program. The students are required to complete a program of advanced courses in engineering.

The Doctoral Program in Applications of Natural Sciences and in Mathematical Engineering is open to graduates holding a Master's Degree who want to extend their scholarly qualification in a relevant field of study. The research-oriented program provides in-depth training for a high level of professional competence in the chosen area (see below) and the ability to develop and use independently the professional knowledge and skills gained in research.

The new study program is focused on nuclear security of nuclear installations, nuclear materials, sources of ionizing radiation, and nuclear forensics. A unique feature of the new Ph.D. program consists in relatedness of nuclear security of nuclear installations, nuclear materials, sources of ionizing radiation, and nuclear safety of nuclear installations and its synergies; particularly in emergency preparedness and forensics methods used in various nuclear fields.

The Doctoral Program in Nuclear Chemistry is intended for graduates of chemistry disciplines of the master course to extend their knowledge, especially of radiochemistry. In its present form, radiochemistry comprises both extensive basic and applied research monitoring chemical and physicochemical aspects of nuclear transformations, as well as methods using radionuclides to tackle chemical problems of a general nature.