The main aim of activities of the branches of vertically integrated Russian Railways JSC is enhancing of manageability and efficiency of business operations. At the current stage, the issue of optimization of costs for product transportation and facilities maintenance in the system of production and technological processes of the railway network has gained relevance. The purpose of this study is development of a mathematical model for the logistic system of transportation, storage, cargo-handling operations, facilities maintenance and reconstruction. Methods of spatial and dynamic modeling in the structure of end-to-end planning of operations were used in the study. Optimization criterion is aggregate cost minimization. Cost function is proposed in the form of local functions of multiple sections along the railway network. The modeling result consists in determining the plans of transportation and supply with minimum costs.