This paper provides a methodology to analyze the seismic performance of different component designs in hybrid masonry structures (HMS). HMS, comprised of masonry panels, steel frames and plate connectors is a relatively new structural system with potential applications in high seismic areas. HMS dissipate earthquake energy through yielding in the steel components and damage in the masonry panels. Currently, there are no complete codes to assist with the design of the energy dissipation components of HMS and there have been no computational studies performed to aid in the understanding of the system energy dissipation mechanisms. This paper presents parametric studies based on calibrated computational models to extrapolate the test data to a wider range of connector strengths and more varied reinforcement patterns and reinforcement ratios of the masonry panels. The results of the numerical studies are used to provide a methodology to examine the effect of connector strength and masonry panel design on the energy dissipation in HMS systems. We use as test cases two story structures subjected to cyclic loading due to the availability of experimental data for these configurations. The methodology presented is however general and can be applied to arbitrary panel geometries, and column and story numbers.