Over the last decades, partial or full collapse of historical buildings has caused loss of the heritage of nations. The failure reasons are varied, starting with deterioration of elements, partial settlements, earthquakes, and extending to wars and blast loadings. This paper presents a numerical investigation of the damaged Gothic architecture church during the famous siege of Famagusta (Cyprus) in 1571 under the effect of internal blast loading. The process from the discharge of the explosion to the partial destruction of the walls is presented, including the propagation of blast waves and impact on the masonry walls. The dynamic response of the structure is evaluated after the effect of relatively high blast loading. Finite Element (F.E.) results are compared to the real damage that was produced by the explosive charge to validate the model. The maximum deflection and principal stresses are evaluated. Results are used to document certain features of failures and provide a practical approach to the progressive collapse of masonry structures under blast loading. The model results are compared to the real damage of the building and show good agreement.