This article describes the experimental and numerical evaluation of the dynamic behaviour of the Cascalheira bridge, located on the Northern Line of the Portuguese railway network. The bridge has a short span formed by two filler-beam half-decks, each one accommodating a railway track. The study includes the development of a finite element numerical model in ANSYS® software, as well as in situ dynamic characterization tests of the structure, namely ambient vibration tests, for the estimation of natural frequencies, modes shapes and damping coefficients, and a dynamic test under railway traffic, particularly for the passage of the Alfa Pendular train. The damping coefficients’ estimation was performed based on the Prony method, which proved effective in situations where the classical methods (e.g., decrement logarithm) tend to fail, particularly in the case of mode shapes with closed natural frequencies, as typically happens with the first vertical bending and torsion modes. The updating of the numerical model of the bridge was carried out using an iterative methodology based on a genetic algorithm, allowing an upgrade of the agreement between the numerical and experimental modal parameters. Particular attention was given to the characterization of the ballast degradation over the longitudinal joint between the two half-decks, given its influence in the global dynamic behavior of this type of double-deck bridges. Finally, the validation of the numerical model was performed by comparing the acceleration response of the structure under traffic actions, by means of numerical dynamic analyses considering vehicle-bridge interaction and including track irregularities, with the ones obtained by the dynamic test under traffic actions. The results of the calibrated numerical model showed a better agreement with the experimental results based on the accelerations evaluated in several measurement points located in both half-decks. In the validation process the vertical stiffness of the supports, as well as the degradation of the ballast located over the longitudinal joint between half-decks, was demonstrated to be relevant for the accuracy and effectiveness of the numerical models.