- Particle and Nuclear Physics🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Systems Programming +1🇨🇿 Bc. | Faculty of Mathematics and Physics
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | Faculty of Social Sciences
- Ancient Egypt and the Near East🇨🇿 Bc. | Faculty of Arts
- Physics🇨🇿 Bc. | Faculty of Mathematics and Physics
- Mathematical and Computational Modelling in Physics🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Computer Graphics, Vision and Game Development +1🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Web and Data Oriented Programming +1🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science with specialisation in Artificial Intelligence +1🇨🇿 Bc. | Faculty of Mathematics and Physics
- Computer Science - Artificial Intelligence🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Computer Science - Language Technologies and Computational Linguistics🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Computer Science - Visual Computing and Game Development🇨🇿 NMgr. | Faculty of Mathematics and Physics
- Comparative Literature +1🇨🇿 NMgr. | Faculty of Arts
- Comparative Literature — East European Studies🇨🇿 NMgr. | Faculty of Arts
- Czech Language and Literature🇨🇿 NMgr. | Faculty of Arts
- Computer Science with specialisation in Programming and Software Development +1🇨🇿 Bc. | Faculty of Mathematics and Physics
- Physiotherapy🇨🇿 Bc. | Faculty of Physical Education and Sport
- Psychology🇨🇿 Bc. | Faculty of Arts
- Humanities and Social Sciences🇨🇿 Bc. | Faculty of Humanities
- 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
- International Masters in Economy, State and Society with specialisation in Politics and the International Economy with respect to Politics🇬🇧 NMgr. | Faculty of Social Sciences
- International Masters in Economy, State and Society with specialisation in Politics and Security🇬🇧 NMgr. | Faculty of Social Sciences
- International Masters in Economy, State and Society with specialisation in History and Society🇬🇧 NMgr. | Faculty of Social Sciences