The article deals with the topical issue of assessing the efficiency of customs administration as one of the tools for the development of the Eurasian Economic Union (hereinafter - the EAEU). It is noted that there are significant differences in approaches to assessing customs administration in the EAEU member states, which creates obstacles to further integration of the EAEU. A comparative analysis of the existing systems for assessing the activities of the customs authorities of the EAEU countries is carried out, which implies the need for unification and standardization of customs operations and procedures, customs administration in general. Based on a comparative analysis of the customs practice of the EAEU countries, as well as existing international experience in unifying the work of customs administrations for the development of economic integration, a proposal was put forward based on the case study of the EU to harmonize the systems for assessing the efficiency of customs administration in the Eurasian Economic Union as a tool for its economic development.