In this paper we propose a planning procedure for serving freight transportation requests in a railway network with fast transfer equipment at terminals. We consider a transportation system where different customers make their requests (orders) for moving boxes, i.e., either containers or swap bodies, between different origins and destinations, with specific requirements on delivery times. The decisions to be taken concern the route (and the corresponding sequence of trains) that each box follows in the network and the assignment of boxes to train wagons, taking into account that boxes can change more than one train and that train timetables are fixed. The planning procedure includes a pre-analysis step to determine all the possible sequences of trains for serving each order, followed by the solution of a 0–1 linear programming problem to find the optimal assignment of each box to a train sequence and to a specific wagon for each train in the sequence. This latter is a generalized assignment problem which is NP-hard. Hence, in order to find good solutions in acceptable computation times, two MIP heuristic approaches are proposed and tested through an experimental analysis considering realistic problem instances.