It is a very difficult engineering issue to assess the earthquake performance levels of existing masonry structures and determine whether they require strengthening or retrofitting. The materials used in the production of masonry structures vary from region to region, even within the same structure, and the lack of standard mechanical properties of these materials makes it difficult to define the material model in the numerical models of such structures. It is known that these problems are eliminated by the Operational Modal Analysis (OMA) technique because it does not damage the structure and accelerates the process. In the framework of this research, experimental measurement of the 5-story masonry structure was taken with OMA, and numerical modeling was made by SAP2000v14 software. The damping ratio, natural frequencies, and mode shapes of the structure were determined. Frequency-domain-based methods were used in the analysis and evaluation of OMA responses from the Enhanced Frequency Domain Decomposition Method (EFDDM), while the Stochastic Subspace Identification Method (SSIM) was used for time-domain-based methods.