The most important contribution to the solution of the main tasks of the country's economic and social development is made by the successful operation of the transport infrastructure. The transport system provides conditions for economic growth, increasing national economy competitiveness and life quality of population. Transport organizations need to continually improve their operations in order to remain competitive. This requires the development of new technologies and methods for doing business, improving the quality of activities and introducing new, modern, effective methods of managing and organizing the activities of enterprises. Business process modeling makes it possible to understand the work and analyze the organization, as well as improve the quality and efficiency of the transport organization. The article discusses different ways aimed at improvement of efficiency and quality of transport organizations. The types of modeling used at transport enterprises are disclosed. Methods for business process modeling in transport organizations are presented. The recommendations of Russian Railways JSC are given in terms of improving the quality and efficiency for the following activities: freight services, freight and commercial services, maintenance of material base, infrastructure services, its maintenance and repair, services for the provision of freight cars, and their maintenance, services for the provision of locomotives and their maintenance and services for the repair of rolling stock. The authors have proposed an algorithm for assessing the efficiency of production processes in railway transport using the example of freight services.