Transition zones corresponding to the passage from railway tracks on embankment to natural ground or settlement free structures are frequently problematic for maintenance. Changing stiffness of the track and differential settlements are the main causes for the degradation of tracks and foundations at transitions. This paper presents a methodology to predict the settlement of the track due to train loading, applicable to transition zones. The methodology is based on dynamic calculations using a (non-linear) train–track interaction model and an incremental settlement model. Important non-linear aspects in dynamic models for railway transitions are the loss of contact between the sleepers and the ballast and the non-linear constitutive behaviour of the ballast. The settlements are calculated paying attention to the factors that most influence the long-term behaviour of ballast, such as the amplitude of the applied dynamic force and the number of loading cycles. The importance of the dynamic loading from the trains and of the constitutive models used for the trackbed layers is analysed.