Structural Health Monitoring (SHM) is of utmost importance for the preservation and safe operation of historical arch bridges. This paper presents the development of a SHM strategy aimed at the model-based damage assessment of masonry bridges using frequency data. Structural damage induces natural frequency changes that are strictly related to the damage location. Consequently, a numerical model capable of reproducing the intact dynamic characteristics should allow to simulate damage scenarios, including the observed one, with the anomaly localisation being performed through the similarity between the experimentally detected frequency changes and the numerically simulated ones. The proposed methodology is based on the availability of an appropriate knowledge of the investigated structure, allowing to define a Finite Element (FE) model that accurately reproduces the system dynamic characteristics. Hence, the SHM strategy involves: (a) the use of the calibrated model to simulate different damage scenarios, so that a Damage Location Reference Matrix (DLRM) is defined through the associated frequency shifts; (b) the damage detection through statistical pattern recognition of vibration data; (c) the damage localisation through the comparison between the identified frequency changes and those defined in the DLRM matrix. Pseudo-experimental monitoring data, referring to a historical masonry viaduct, were generated and used to exemplify the reliability and accuracy of the developed algorithms in detecting and localizing damage.