The rapid growth of online trade leads to a number of problems faced by EAEU member states in the implementation of customs regulation of electronic commerce: reducing the tax base by reducing traditional trade; sending profit fl ows to those countries where the parent companies of online trading platforms are registered; imperfect competition of goods imported duty-free compared to goods produced within the EAEU; the emergence of new security threats due to the actual lack of certification and other restrictions, which actualizes a thorough study of this phenomenon and its timely regulation. The article outlines topical issues of regulating the movement of goods of cross-border electronic trade across the customs border of the EAEU, which make it necessary to amend the Agreement on the Customs Code of the EAEU on cross-border electronic commerce, that is, the content of the draft Protocol on Amendments, according to which "goods for electronic commerce" is understood as goods, acquired by individuals in the framework of foreign electronic commerce, under which, in turn, it is meant to conclude a transaction, one of the parties to which is a foreign economic operator, on electronic trading platforms through the Internet. An analysis of these changes is presented, in particular, the prospect of creating a new legal institution and type of activity in the field of customs regulation — an e-commerce operator, which will provide logistics of operations, as well as ensure interaction with Internet sites and customs, ensuring customs declaration processes. The main requirements for the operator of electronic commerce, the specifics of temporary storage, customs declaration and issuance of electronic commerce goods, the specifics of the application of the customs procedure of the customs warehouse, as well as the procedure for applying customs payments and the prospects for regulating electronic commerce in the EAEU have been determined.