- Geopolitical Studies🇬🇧 NMgr. | Faculty of Social Sciences
- Mathematics for Information Technologies +1🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Bioinformatics🇨🇿 Bc. | Faculty of Science
- General Mathematics🇨🇿 Bc. | Faculty of Mathematics and Physics
- Mathematical Modelling🇨🇿 Bc. | Faculty of Mathematics and Physics
- 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
- Archaelogy of Prehistory and Middle Ages with double curriculum study Intercultural Communication: Translation and Interpreting with specialisation in English for Translation and Interpreting🇨🇿 Bc. | 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
- German and Central European Studies🇨🇿 NMgr. | Faculty of Social Sciences
- Computer Science🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Computer Graphics, Vision and Game Development🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in General Computer Science🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Programming and Software Development🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Systems Programming🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Web and Data Oriented Programming🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Artificial Intelligence🇨🇿 Bc. | Faculty of Mathematics and Physics
- Teacher Education of Physical Education for Upper Secondary Schools +1🇨🇿 NMgr. | Faculty of Physical Education and Sport
- Teacher Education of Physical Education for Upper Secondary Schools with double curriculum study Teacher Education of Geography for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Physical Education and Sport
- Teacher Education of Physical Education for Upper Secondary Schools with double curriculum study Teacher Education of Mathematics for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Physical Education and Sport
- Evolutionary Biology🇨🇿 NMgr. | Faculty of Science
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences