The aim of the research is to classify the European Union (EU) countries based on the progress in the economic performance of agriculture. The originality of the paper stems from the fact that a new set of indicators (in relative form) was used to identify the clusters. The following indicators are used to assess the economic performance of the EU agricultural sector (by cluster analysis) for two periods (2015–2017 and 2018–2020): total labor force input, real income of factors in agriculture per annual work unit, total agricultural output, gross value added of the agricultural industry, and animal output. The study confirmed that EU countries, according to changes in agricultural performance, differ significantly. They were grouped into four relatively homogeneous clusters according to their similarity, with a clear geographical dispersion for both analyzed periods. Identifying development disparities between EU countries can be useful in future redesigns of the Common Agricultural Policy measures in terms of increased support to certain members.