The long-term performance of the railway track is an important factor to be taken into account in the design in order to prevent excessive maintenance costs. Therefore, the prediction and control of the permanent deformation of the substructure are key aspects in the analysis and design of railway track structures. In this paper, the influence of permanent deformations of the substructure on ballasted and ballastless tracks is studied through the numerical modelling. It is intended to study the phenomenology involved, namely, the stress path and its influence in the permanent deformation and long-term behaviour. The numerical model is based on the 2.5D formulation, supported by the FEM-PML (Perfect Matched Layers). The evolution of the stress level (and the stress path in particularly) induced by the train is one of the most important factors involved in the permanent deformation laws. Two loading conditions are analysed related to the passage of two trains with different axle loads, geometry and speed: a conventional passenger train (Alfa Pendular) and a freight train.