- International Masters in Economy, State and Society with specialisation in Economy and Business🇬🇧 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
- Deaf Studies🇨🇿 Bc. | Faculty of Arts
- Dentistry🇨🇿 Mgr. | Faculty of Medicine in Pilsen
- Religion and Social Sciences for Teacher Education🇨🇿 Bc. | Hussite Theological Faculty
- Economics and Finance with specialisation in Central Banking and Financial Regulation🇨🇿 NMgr. | Faculty of Social Sciences
- Economics and Finance with specialisation in Financial Markets and Data Analysis🇨🇿 NMgr. | Faculty of Social Sciences
- Economics and Finance with specialisation in Banking and Corporate Finance🇨🇿 NMgr. | Faculty of Social Sciences
- Economics and Finance with specialisation in Economics of Public Sector and Health Care🇨🇿 NMgr. | Faculty of Social Sciences
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences
- Psychology with special pedagogy extension🇨🇿 Bc. | Faculty of Education
- 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 Security🇬🇧 NMgr. | Faculty of Social Sciences
- Evolutionary Biology🇨🇿 NMgr. | Faculty of Science
- Special Education +1🇨🇿 Bc. | Faculty of Education
- Catholic Theology +1🇨🇿 PhD. | Catholic Theological Faculty
- Clinical and Toxicological Analysis🇨🇿 NMgr. | Faculty of Science
- Reproduction and Developmental Biology🇨🇿 NMgr. | Faculty of Science
- Biochemistry and Pathobiochemistry🇨🇿 PhD. | First Faculty of Medicine
- Demography +1🇨🇿 NMgr. | Faculty of Science