The locomotive assignment and the freight train scheduling are important problems in railway transportation. Freight cars are coupled to form a freight rake. The freight rake becomes a train when a locomotive is coupled to it. The locomotive assignment problem assigns locomotives to a set of freight rakes in a way that, with minimum locomotive deadheading time, rake coupling delay and locomotive coupling delay all freight rakes are hauled to their destinations. Scheduling freight trains consists of sequencing and ordering freight trains during the non-usage time between passenger trains but with no interference and with minimum delay times. Solving these two problems simultaneously is of high importance and can be highly effective in decreasing costs for rail transportation. In this paper, we aim to minimize the operational costs for the locomotive assignment and the freight train scheduling by solving these two problems concurrently. To meet this objective, an efficient and effective algorithm based on the ant colony system is proposed. To evaluate the performance of the proposed solution method, twenty-five test problems, which are based on the conditions of Iran Railways, are solved and the computational results are reported.