The Institute of Political Studies of Charles University offers two doctoral programmes, in Political Science (under the auspices of the Department of Political Science) and in International Relations (under the auspices of the Department of International Relations). Doctoral studies are accredited for four years in both full-time and combined forms. Both types of studies can be completed on the basis of valid accreditation either in Czech or in English. The study in English is subject to a fee.

The aim of the four-year Ph.D. programme is to prepare highly qualified professionals capable of participating in basic and applied research in academic departments and universities, but also to engage in work in the public sector, in analytical activities of relevant government departments and in various types of mass media or in the private sector in the Czech or international environment.

Doctoral studies at IPS are based mainly on the independent scientific and research work of the doctoral student. The result of this research then forms the dissertation. In addition, each student should publish at least two professional articles during their studies, participate in research and scientific activities in the form of grant applications, participation in conferences, etc. During their studies, Ph.D. students have the opportunity to engage in teaching activities at the faculty. 

Selected full-time Ph.D. students can become academic staff members within the Centre for Doctoral Studies (CDS) during their studies, providing them with additional financial support for their research. Within the CDS, these students also participate in the organisational support of doctoral studies at the Institute of Political Studies. The CDS selection process takes place once a year and is open to first-year students.

The structure of the doctoral studies is determined by an individual study plan, which the doctoral student prepares in cooperation with his/her supervisor at the beginning of the first year and which is then submitted to the departmental board for approval. With the consent of the supervisor and after adding to the individual plan, doctoral students may enrol in elective courses according to their professional interest; however, within each field of study, there are defined compulsory seminars that each doctoral student must take.

The course of study, the state final examination and the defence of the doctoral dissertation are regulated by the Study and Examination Regulations of the Charles University, the Rules for The Organization of Study on FSS CU, the Dean's Measure No. 5/2021 Organisation of Doctoral Studies at the Charles University Faculty of Arts and the framework study plans for individual disciplines.

The admission procedure for doctoral studies is held once a year in June and enrollment in the study programme is in September of the following academic year.