In this paper, a three-dimensional numerical model is applied for studying railway vibrations. The numerical model is based on finite element method formulated in the time domain with an implicit scheme of integration. In the first part of the paper the numerical approach is briefly described. An uncoupled scheme is applied: (i) firstly the train loads are calculated taking into account dynamic excitation with a 2D vehicle-track model; (ii) the computed loads on each sleeper are introduced into a 3D numerical model, developed in the commercial code Plaxis, which is used to simulate the wave propagation in the ground. In the second part of the paper a real case study, located in Portugal, is presented, being used for the experimental validation of the proposed model. The numerical results of ground vibrations show an acceptable agreement with real measurements. Therefore, the proposed approach can be used as a reliable prediction tool based on PLAXIS software, which allows simulating railway vibrations in some specific cases such as soft soils, inhomogeneous geometries in the longitudinal direction of the track and transition zones.