- Teacher Education of Czech Language and Literature for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Arts
- European Politics and Society: Vaclav Havel Joint Master Programme🇬🇧 NMgr. | 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
- Parasitology and Infection Biology🇬🇧 NMgr. | Faculty of Science
- Teacher Education of Geography for Upper Secondary Schools with double curriculum study Teacher Education of Biology for Upper Secondary Schools🇨🇿 NMgr. | Faculty of Science
- General Mathematics🇨🇿 Bc. | Faculty of Mathematics and Physics
- 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
- Germanic and North European Studies with specialisation in German Studies with double curriculum study Central European Studies with specialisation in Hungarian Studies🇨🇿 Bc. | Faculty of Arts
- Germanic and North European Studies with specialisation in German Studies with double curriculum study Central European Studies with specialisation in Slovak Studies🇨🇿 Bc. | Faculty of Arts
- Germanic and North European Studies with specialisation in Scandinavian Studies with double curriculum study Central European Studies with specialisation in Hungarian Studies🇨🇿 Bc. | Faculty of Arts
- Germanic and North European Studies with specialisation in Finnish Studies with double curriculum study Central European Studies with specialisation in Hungarian Studies🇨🇿 Bc. | Faculty of Arts
- Germanic and North European Studies with specialisation in Dutch Studies with double curriculum study Central European Studies with specialisation in Hungarian Studies🇨🇿 Bc. | Faculty of Arts
- History of Christian Art +1🇨🇿 Bc. | Catholic Theological Faculty
- Communication Studies🇨🇿 Bc. | Faculty of Social Sciences
- Communication Studies with specialisation in Media Studies🇨🇿 Bc. | Faculty of Social Sciences
- Communication Studies with specialisation in Journalism🇨🇿 Bc. | Faculty of Social Sciences
- Communication Studies with specialisation in Marketing Communication and Public Relations🇨🇿 Bc. | Faculty of Social Sciences
- Geoinformatics, Cartography and Remote Sensing🇨🇿 NMgr. | Faculty of Science
- Social Medicine +1🇨🇿 PhD. | Faculty of Medicine in Pilsen
- Mathematical and computer modeling +1🇨🇿 PhD. | Faculty of Mathematics and Physics