In the last 30 years, the scientific community has developed and proposed different models and numerical approaches for the study of vibrations induced by railway traffic. Most of them are formulated in the frequency/wave number domain and with a 2.5D approach. Three-dimensional numerical models formulated in the time/space domain are less frequently used, mainly due to their high computational cost. Notwithstanding, these models present very attractive characteristics, such as the possibility of considering nonlinear behaviors or the modelling of excess pore pressure and non-homogeneous and non-periodic geometries in the longitudinal direction of the track. In this study, two 3D numerical approaches formulated in the time/space domain are compared and experimentally validated. The first one consists of a finite element approach and the second one of a finite difference approach. The experimental validation in an actual case situated in Carregado (Portugal) shows an acceptable fitting between the numerical results and the actual measurements for both models. However, there are some differences among them. This study therefore includes some recommendations for their use in practical soil dynamics and geotechnical engineering.