Транспортная инфраструктура является одним из факторов социально-экономического и пространственного развития территорий. Принятый в 2018 г. комплексный план модернизации и расширения магистральной инфраструктуры призван разрешить ряд инфраструктурных проблем России, обеспечить развитие транспортных коридоров, повышение экономической связанности. В ходе исследования выявлено, что, несмотря на достижение ряда позитивных изменений в магистральной инфраструктуре, полноценная реализация плана может быть поставлена под угрозу, что обусловлено рядом системных и организационных рисков и проблем. The developed transport infrastructure is one of the factors for the Russian Federation socio-economic and spatial development, as it ensures the area-to-space relationship, helps to reduce the economic distance and increase the migration and transport mobility of the population, etc. However, to implement these objectives successfully, it is necessary to expand and modernize the transport infrastructure, taking into consideration the promising trends. A significant role is assigned to the Federal strategic documents that set out the main provisions, forms, methods and tools for implementing the state policy. The purpose of the article is to identify and systematize risks in implementing the Comprehensive plan for upgrading and expanding the trunk infrastructure until 2025 based on the results of the first full year of its implementing. Methods of monographic, comparative analysis and synthesis, economic and statistical analysis were used during the research. As a result, it was found that the implementation of the Comprehensive plan may be jeopardized, mainly due to non-compliance with the project deadlines as well as due to the institutional risk problems, which were highlighted: inadequate regulatory and methodological framework, that complicates the implementation; difficulties in monitoring the implementation; low level of the list of activities coordination. There are organizational problems and obstacles to the implementation of the plan containing the provisions of the Russian Federation President Decree of May 7, 2018 No. 204 "On the national goals and strategic objectives for the Russian Federation development for the period untill 2024". Studying the plan settings and the main outcomes of its implementation as well as the results of the content analysis of the experts and scientists expert opinions allowed to identify and substantiate the key risks and challenges in the implementation of the Comprehensive plan, which will help to achieve the set goals and objectives. The results of the work can be used by researchers in conducting their research on similar topics, as well as in the activities of the Federal and regional authorities in the development and adjustment of strategies and programs for socio-economic, transport and spatial development.