Digital technologies optimize certain aspects of customs operations, but also change the functional purpose of customs, raising its role in ensuring the transparency of international trade. The aim of the study was to assess the impact of factors measured by the Organisation for Economic Co-operation and Development (OECD) trade facilitation indicators on the transparency of customs operations. The study employed correlation, regression analyses, and analysis of variance (ANOVA). The study provides an integrated empirical analysis of the complex impact of technological, operational, and regulatory factors on the transparency of customs operations. The results revealed that the automation of customs procedures with a regression coefficient for the corresponding indicator of 0.3132 had the strongest positive impact on the availability of information (transparency of customs operations). A strong impact of the opportunities and methods for appealing administrative decisions of border authorities (0.2688), as well as simplifying customs control procedures and introducing “single windows” (0.2384) was observed. A less considerable, but statistically significant impact was shown by compliance with the discipline of fees, payments, and fines (0.1438) and simplification and standardization of trade documentation (0.1366). It is concluded that strategies for increasing the transparency of customs operations should focus on the above factors, while increasing the effectiveness of areas that did not show a significant impact on transparency. These are the involvement of the trade community, interaction between internal and external border agencies, the development of Advance rulings, as well as ensuring good governance and impartiality. The effectiveness of these areas should be increased by improving the mechanisms for their provision at the national and international levels. The results of the study are useful for determining priority areas of strategies for increasing the transparency of customs operations, especially regarding the development of digital platforms, for example, accelerating automation, developing single windows, etc.