The growth in international trade volumes and the digitalization of customs procedures make the study of the of NCTS’s impact on the development of customs logistics in the context of common transit relevant. The purpose of the article is to study the functioning of NCTS and its impact on customs logistics, taking into account information-technological, operational-procedural, economic, organizational-institutional, and international aspects. The study uses methods of analysis and synthesis, systemic, structural-functional, comparative approaches, and the generalization method. The architecture and principles of the functioning of NCTS are revealed, its advantages and challenges for customs authorities and entities of foreign economic activity are systematized. The dynamics of the implementation of NCTS in Ukraine in 2022-2025 were analyzed, which showed a significant increase in the volume of transit declarations and increased integration into the European customs space. The main consequences of the functioning of NCTS for customs logistics were determined, in particular, increasing the transparency of transit flows, accelerating customs procedures, reducing transaction costs, and strengthening coordination between customs administrations. At the same time, challenges associated with the system’s technical complexity, the need to develop digital infrastructure, cybersecurity and digital competencies of users were outlined. A conceptual model of the impact of NCTS on customs logistics was proposed. The theoretical significance of the results lies in the development of scientific approaches to the study of digital transit systems, and the practical significance lies in the possibility of using the results to improve customs policy and adapt the national customs system to common transit standards.