Diploma thesis is focused on analysis of funding of university education in The Slovak Republic and The Czech Republic. The first chapter contains definitions of fundamental aspects of main focuses of diploma thesis such as education, funding of enterprises in general and issues of funding of university sphere. In this chapter we also discuss progress of law about universities in Slovakia and in The Czech Republic. The forth chapter of the thesis is focused on analysis of funding public universities in both countries. In this chapter we also define incomes included in budget of public universities which according to the law can be shown by university itself. The data from annual reports of Ministry of education, science, research and sport of The Slovak Republic and Ministry of education, youth and sports of The Czech Republic were base of our final assessment. These reports contain the information about specific amount of financial funding for individual chapters or programs which are assign according to budget of particular country and university. Conclusion of chapter is dedicated to aspects which have influence on amount of funding such as number or mobility of students and pedagogical employees. Result of this diploma thesis is evaluation of development in funding education in both countries in 5 year long period.