The recent seismic activity in Croatia has inflicted significant damage upon numerous buildings, with masonry structures being particularly affected. Consequently, experimental investigations and structural condition assessments’ have garnered increased attention, as they have become integral to the renovation process for such buildings. Additionally, assessing the structural condition prior to seismic events is vital for determining the extent to which earthquakes impact the stiffness of systems, such as masonry structures. This paper presents the results of experimental investigations and numerical analysis conducted on a damaged high school building in Sisak, Croatia. The experimental investigation involved shear testing, flat jack analysis, and operational modal analysis. Utilizing the available drawings and mechanical properties determined experimentally, an initial numerical model was developed. Subsequently, through the iterative process of finite element model updating, the initial numerical model was refined based on the structural dynamic properties. The updated numerical model was then employed to assess the structural condition prior to the earthquake event. This study contributes to the field by providing insights into the post-earthquake estimation of dynamic properties in intact masonry buildings, utilizing a comprehensive approach that combines experimental investigations and finite element model updating. By quantifying the changes in dynamic parameters, such as natural frequencies and mode shapes, the study provides valuable insights into the response characteristics of damaged masonry building. The observed differences in natural frequencies between the damaged and undamaged states are as follows: 9% for the first mode shape, 6% for the second mode shape, and 2% for the third mode shape.