Restoration and retrofitting of heritage buildings is a complex analysis. In actual practice, building materials of heritage masonry buildings are anisotropic. However, in practice, these building materials had been considered isotropic to optimize the analysis. The present study is a comparative analysis of these two approaches. A heritage school building in northern India underlying seismic zone IV has been considered for the analysis. The seismic performance analysis of the buildings has been carried out through numerical modeling using the SAP2000. Analysis has been carried out for one set of isotropic and three sets of orthotropic material parameters. Normal and shear stresses had been observed and compared with stress calculated from the empirical relationships provided in the standard code of practice.