- Particle and Nuclear Physics🇨🇿 NMgr. | Faculty of Mathematics and Physics
- International Masters in Economy, State and Society with specialisation in Politics and Security🇬🇧 NMgr. | Faculty of Social Sciences
- 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
- Master in Area Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Social Work🇨🇿 NMgr. | Faculty of Arts
- 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
- International Masters in Economy, State and Society with specialisation in History and Society🇬🇧 NMgr. | Faculty of Social Sciences
- Finance and Data Analytics🇬🇧 NMgr. | Faculty of Social Sciences
- German Language for Teacher Education🇨🇿 Bc. | Faculty of Education
- Master in Economic Research🇨🇿 NMgr. | Faculty of Social Sciences
- Mathematical and Computational Modelling in Physics🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Theoretical Physics🇨🇿 NMgr. | Faculty of Mathematics and Physics
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 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
- Law and Jurisprudence🇨🇿 Mgr. | Faculty of Law
- History and Area Studies🇬🇧 Bc. | Faculty of Social Sciences
- Social Sciences🇬🇧 Bc. | Faculty of Social Sciences
- Politics, Philosophy and Economics🇬🇧 Bc. | Faculty of Social Sciences
- Area Studies with specialisation in Area Studies🇨🇿 Bc. | Faculty of Social Sciences
- Molecular Biology and Biochemistry of Organisms🇨🇿 Bc. | Faculty of Science
- Ecological and Evolutionary Biology🇨🇿 Bc. | Faculty of Science
- Bioinformatics🇨🇿 Bc. | Faculty of Science
- Biology🇨🇿 Bc. | Faculty of Science