Public universities in the Czech Republic are largely financed by public expenditure. To increase the quality of higher education, it is essential to link education with scientific research and economic practice. To make the educational process more efficient, it is inevitable to connect theory and practice to allow graduates to integrate into the labor market.

The research aims to compare the efficiency of all 26 public universities in the Czech Republic and to recognize how efficiently they operate. The data were retrieved from publicly available databases of the Ministry of Education, Youth and Sports and the Educational Policy Center of the Faculty of Pedagogy of Charles University.

The non-parametric method of mathematical programming allows to calculation of the relative efficiency of completely homogeneous and comparable units based on specified criteria, which was used to evaluate the efficiency. A non-oriented slacks-based measure model with constant returns to scale was chosen. The number of employees and the average monthly salary of the university’s employees were selected as input variables. The number of Master’s degree graduates and the number of employed Master’s degree graduates were selected as output variables. Furthermore, the change in efficiency for the years was calculated based on the Malmquist index.

The results showed that only four universities were fully efficient in the monitored period. These fully efficient schools produce approximately 40% of the total number of Master’s degree graduates. Furthermore, based on the Malmquist index, it was found that only two public universities achieved an improvement during the monitored period.

Keywords: Data envelopment analysis, efficiency, higher education, public universities.