Many countries have focused on the improvement of education system performance. Small number of studies consider system of a country as unit of assessment where indicators represent all levels of education system. In the paper, we propose the methodology for the performance analysis of education systems as a whole hybridizing Data Envelopment Analysis and Principal Component Analysis. Its applicability is illustrated by the analysis of the data collected for 29 European countries. In the analysis we used publicly available data from EUROSTAT and OECD which European Commission uses for the performance monitoring of education in European Union. No prior assumptions were made or expert judgements included. We demonstrated good performance of the method on limited data set. The proposed methodology of hybrid Data Envelopment Analysis and Principal Component Analysis allows researchers analyse education systems quantitatively. The recommendations for improvements and assessment of real world education systems should be based on the analysis of a sufficiently large data set comprehensively representing the considered education systems.