- Child and Adult Nutrition🇨🇿 NMgr. | First Faculty of Medicine
- Jewish Studies with double curriculum study Religious Studies🇨🇿 NMgr. | Hussite Theological Faculty
- Area Studies with specialisation in Balkan, Eurasian and Central European Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in European Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in German and Austrian Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in North American Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Area Studies with specialisation in West European Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Balkan, Eurasian and Central European Studies with specialisation in Russian and Eurasian Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Balkan, Eurasian and Central European Studies with specialisation in Balkan and Central European Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Master in Area Studies🇬🇧 NMgr. | Faculty of Social Sciences
- International Masters in Economy, State and Society with specialisation in Politics and the International Economy with respect to Economy🇬🇧 NMgr. | Faculty of Social Sciences
- International Masters in Economy, State and Society with specialisation in Politics and Security🇬🇧 NMgr. | Faculty of Social Sciences
- Teacher Education of Geography for Upper Secondary Schools with double curriculum study Teacher Education of Biology for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Science
- Hydrology and Hydrogeology🇨🇿 Bc. | Faculty of Science
- Physical Geography and Geoecology🇨🇿 NMgr. | Faculty of Science
- Area Studies with specialisation in Area Studies🇨🇿 Bc. | Faculty of Social Sciences
- Czech-German Studies🇨🇿 Bc. | Faculty of Social Sciences
- Law and Jurisprudence🇨🇿 Mgr. | Faculty of Law
- Public and Social Policy Studies🇬🇧 NMgr. | Faculty of Social Sciences
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences
- Catholic Theology +1🇨🇿 PhD. | Catholic Theological Faculty
- Preventive Medicine and Epidemiology +1🇨🇿 PhD. | Third Faculty of Medicine
- Landscape and Society🇨🇿 NMgr. | Faculty of Science
- Economics and Econometrics🇨🇿 PhD. | Faculty of Social Sciences
- Gynaecology and Obstetrics +1🇨🇿 PhD. | Faculty of Medicine in Pilsen
- Evolutionary Biology🇨🇿 NMgr. | Faculty of Science
- Computer Science with specialisation in Systems Programming🇨🇿 Bc. | Faculty of Mathematics and Physics