Searching for achieving an ambitious reduction in greenhouse gas emissions, the EU has set as a goal a modal shift in freight transport of 30% by rail for the near future. In this context, it is vital to use modal choice models road versus rail to assess the shippers’ acceptance of the actions promoting the use of rail. This paper develops a combined model for jointly evaluating modal split and railway freight flows, addressed to the case when a modal split based on a random utility model is available, and some of its coefficients may present a non-negligible variability. To this end, after the initial deterministic formulation a robust counterpart of the model is developed. The model, formulated as a non-linear integer programming problem, is oriented to a multi-carrier environment and includes constraints to consider the interactions between the different types of flows on the railway network, allowing a good evaluation of the cost types of the carriers and the network capacity. An algorithmic solution based on the outer approximation method is shown to provide accurate solutions in a reasonable computational time for the robust and non-robust versions of the model. Examples centered on a section of the Trans-European Transport Network, the TEN-T Core network corridors, are reported to test the model’s applicability. Results show that this model can be a helpful tool for analyzing the possible shippers’ response to the different railway carriers’ services competing with the road.