- International Master in Security, Intelligence and Strategic Studies (IMSISS)🇬🇧 NMgr. | Faculty of Social Sciences
- Geopolitical Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Political Science🇨🇿 NMgr. | Faculty of Social Sciences
- Central European Studies with specialisation in Hungarian Studies🇨🇿 NMgr. | Faculty of Arts
- Central European Studies with specialisation in Hungarian Studies and Slovak Studies🇨🇿 NMgr. | Faculty of Arts
- Central European Studies with specialisation in Hungarian Studies with double curriculum study South East European Studies🇨🇿 NMgr. | Faculty of Arts
- Coach🇨🇿 Bc. | Faculty of Physical Education and Sport
- Law and Jurisprudence🇨🇿 Mgr. | Faculty of Law
- Gender Studies +1🇨🇿 NMgr. | Faculty of Humanities
- Chinese Studies🇨🇿 Bc. | Faculty of Arts
- General Medicine🇨🇿 Mgr. | Second Faculty of Medicine
- Public and Social Policy Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Public and Social Policy🇨🇿 NMgr. | Faculty of Social Sciences
- Humanities and Social Sciences🇨🇿 Bc. | Faculty of Humanities
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences