Taxation of foreign economic operations is carried out by applying tariff and non-tariff regulatory methods and is based on the use of tax policy instruments -customs duty, excise duty and VAT. Having defined its foreign economic and tax policy, the state determines the direction for development, as well as the strategy and tactics to achieve the goal through foreign economic operations. Based on the generalization of theoretical foundations, it is determined that foreign economic operations are a type of foreign economic activity aimed at implementing a trade agreement between countries. The customs duty is of the utmost importance in taxation. By economic nature, it is an integral part of the taxation of foreign economic operations. During the research process the economic importance of customs duty was deepened and determined that, unlike other indirect taxes, which are primarily aimed at fiscal purposes, customs duty is a tool for financial regulation of the country's economy, namely it stimulates inefficient domestic production and perform other functions for foreign trade development. The theoretical, methodological and practical provisions concerning taxation of foreign economic operations with agricultural products and assessment of its functioning efficiency in conditions of Ukrainian integration into the EU are studied. A comprehensive approach to the implementation of the regulation in foreign economic operations with agricultural products is proposed. The directions to improve taxation of foreign economic operations are substantiated.