The priority goals of the development of Czech higher education include ensuring the quality of its activities, improving the availability and relevance of flexible forms of education, and increasing efficiency in teaching and research. Several professional articles evaluated educational efficiency, but the proposed models did not include unemployed graduate students. The paper assesses education efficiency at public universities in the Czech Republic in 2020-2021 using an extended Data envelopment model with undesirable outputs, non-proportional and non-radial measures of distance from the efficient frontier. The influence of selected economic, social, regional and institutional factors on education efficiency is estimated by a panel regression model using the Feasible generalized least squares method. The results document the level and development of education efficiency and find insufficient reduction of unemployed graduates as a critical problem of inefficiency. More prominent universities achieve higher education efficiency. The main statistically significant factors influencing changes in education efficiency are population density, the unemployment rate, the location of the university in larger urban centres and the number of students per university employee.