Seismic isolation technology is one of the novel developments in the construction technology to increase the earthquake resistance of structural systems. In this study, it is intended to strenghten a historical masonary mosque system with base isolation technique. As a historical masonry system, Sehzade Mehmet Mosque which is considered as the apprenticeship of Mimar Sinan is considered and modeled with the finite element method. This masonry system is investigated for fixed base and seismically isolated bases with lead rubber bearing and high damping rubber bearing. Dynamic analyses of these systems are performed with the response spectrum method and the resulting structural periods and responses are compared with each other. Results obtained from the study show that seismic base isolation technique applied to the historical masonry system improves the dynamic behavior of the system. It is also concluded that the seismic base isolation technique is a proper method to strengthen historical systems without damaging the original historical texture.