After the construction of the Keban Dam, some settlements with historical, cultural, and natural value were flooded. A scientific committee consisting of academicians and public authorities decided to the relocation of the buildings including the historical Çelebiağa Mosque. In this study, the seismic soil-structure interaction analysis of the historical Çelebiağa Mosque, which was dismantled and reconstructed in a separate region due to the construction of the Keban Dam was carried out. The analysis of the masonry mosque was performed with the SAP2000 finite element analysis software. The Winkler foundation model was used to idealize the soil environment on which the historical mosque was built. The effects of soil-structure interaction on historical masonry mosque were examined in terms of transmitted acceleration, response spectra, and lateral displacement at various heights of the structure. Depending on the results of the analysis, the effects of soil-structure interaction of a reconstructed historical masonry building were investigated. PGA was obtained as 0.51g at the flag level of the minaret under the Kocaeli earthquake and 0.94g under the Sivrice earthquake. Again, the maximum horizontal displacements of the minaret at the flag level were obtained as 11 cm and 8.5 cm under the Kocaeli and Sivrice earthquakes. The behavior of historical masonry structures under earthquake loads has been interpreted by considering the geological conditions.