The structural assessment of masonry arch bridges is often hindered by uncertainties related to geometry, materials, and loading conditions, particularly under seismic actions. This study proposes a modelling strategy that enables advanced numerical analysis of such structures through the calibration of a simplified finite element model. Using the San Marcello Pistoiese bridge in Italy as a case study, two models are developed: a detailed three-dimensional solid model and a reduced shell-based model referred to as the Shell-Box Model (SBM). Both models implement the Concrete Damage Plasticity (CDP) approach to capture the non-linear behavior of masonry materials. The SBM, once calibrated against the solid model with the regard to the modal characteristics, has been used to perform nonlinear analyses in the static and dynamic field, under natural accelerograms, demonstrating a good capability of reproducing the significant structural response features, including capacity curves and damage maps - while reducing computational effort by over 99%. This makes the simplified model particularly suitable for large-scale parametric analyses aimed at uncertainty management.