Mitigating vulnerabilities of cultural heritage assets prevents damage from extreme weather, encourages sustainable restoration practices that cut carbon emissions, and yields long-term cost savings, all while conserving the legacy of historical constructions. Developing a precise numerical model that closely simulates the actual structure is a crucial component of a vulnerability assessment methodology. The objective of this study is to present a finite element (FE) model updating of a historical masonry arch with a corner tower in Rhodes, Greece. The Naillac tower, as part of the medieval city of Rhodes, is recognized as a UNESCO World Heritage site. Three-dimensional (3D) documentation was conducted using digital cameras, 3D laser scanners, drones, and total stations. These tools were chosen for their effectiveness in capturing the intricate architecture of the structure while expediting the documentation process. A 3D dense point cloud was generated, forming the basis for the subsequent development of a 3D FE model. On the other hand, operational modal analysis (OMA) was conducted based on the ambient vibration testing (AVT) data using accelerometer sensors to define the frequency values and corresponding mode shapes of the structure. The material properties of the FE model are calibrated to match the modal properties of the FE model with those recorded experimentally. Finally, the updated mechanical properties of the stone masonry for different parts of the structure were presented. Significant variations exist between the calibrated material properties and those assumed from empirical equations, underscoring the necessity for model calibration based on OMA.