The article discusses the innovative development of transit transportation on the railway transport of Kazakhstan, including the management of domestic, export-import and transit cargo transportation. The study revealed the need to create a modern transport infrastructure of Kazakhstan to attract transit cargo flows. Currently, experts in Kazakhstan identify the following issues for rail transport: limited international transportation, limited technological development, insufficiently developed intermodal transportation, low level of transport and logistics services, incompetent number of vehicles and their outdated fleet. At the same time, logistics makes a significant contribution to GDP in developed countries, while it is still at a low level in Kazakhstan. The article discusses the fundamental changes in all technological and business processes in Kazakhstan’s railway transport, based on the introduction of new rolling stock, efficient technological infrastructure facilities, intelligent transportation process management systems and other technological and organizational innovations. The main feature of railway transport is that it affects the pace and scale of innovation activity at the enterprises of the industry, therefore railways belong to the infrastructure and are focused on their main maintenance. The necessity of these changes in increasing the competitiveness of enterprises in the target industry, increasing the efficiency of their functioning and investment attractiveness is being studied. In this context, one of the important and difficult tasks is to develop approaches to managing the development of innovation activity at the enterprises of the industry. A set of organizational and economic measures is considered in relation to railway transport enterprises by public administration bodies to manage the innovative development of transit transportation, the formation of internal and external conditions for the growth of innovative activity.