Abstract Although underpasses are low-cost solutions widely used in high-speed railway lines, their dynamic analysis is complex given the large number of variables involved in the problem and the high computational cost of detailed 3D models. The objective of this study is therefore to present a simple and fast 3D method for estimating the dynamic behavior of culvert-type underpasses subjected to dynamic loads induced by high speed trains under normal operating conditions. This model was adjusted to data gathered in situ during a measurement campaign on the high-speed line between Segovia and Valladolid in Spain. The prediction method is based on a sub-structuring approach with three key ingredients: an emission 2D finite element model that simulates the track; a slab model based on Kirchhoff theory and the Rayleigh-Ritz method using trigonometric shape functions; and sidewall-models using a formulation of a finite-length beam on a viscoelastic foundation. The emission model estimates the contact forces for the slab using the vertical dynamic behavior of the railway track, and the slab model accounts for the contribution of the soil-structure interaction that takes place at the sidewalls by means of the frequency-dependent stiffness at the corresponding joints.