In this paper, we examine the freight scheduling problem and the design of decision support systems in rail transport. We present an intelligent control system that solves the engine and crew scheduling problem. The problem of freight scheduling is modelled as an assignment and optimization problem and solved using two different algorithms: the method of auctions and the simulated annealing method. The algorithms were adopted in order to optimize the solution while accounting for domain-specific features of rail transportation technology. A comparative evaluation of the two approaches allowed us to design a hybrid combined method which we apply in the development of an intelligent transport control system for scheduling rail traffic across the East Siberian Railway.