In the scope of this paper, it is aimed to compare the effects of near and far-fault earthquakes on the seismic responses (amplitude, spectrum effect, stress) of a relatively complex historical stone masonry mosque (125-years old Kurtulus Mosque, Gaziantep-Turkey) through soil-structure-interaction (SSI) analysis as well as fixed base solution. The SSI analysis (using direct approach) has also been performed for the effect of boundary types (viscous, elementary) of substructure. A 3D finite element modeling of mosque and substructure soil is built with solid elements, and then the seismic responses of mosque are evaluated by time-history analysis. The near and far-fault motions, which have approximately identical peak ground accelerations from same earthquake, are selected by representing their own characteristics (i.e., velocity, distance, etc.) from the strong ground motion records in previous earthquakes (1979 Imperial Valley, 1992 Erzincan, 1999 Chi-Chi, 1999 Kocaeli, 2010 Darfield). It is found from the results that both the near and far-fault earthquakes mostly lead to the responses similarly significant for both the fixed base and SSI considerations. However, regarding the resonance effect on the mosque, the far-fault motion appears more prominent in fixed base solution. Moreover, the far-fault motions mostly result in high amplitudes in the viscous boundary of SSI compared to the elementary boundary. When compared to the fixed base and SSI due to the near and far-fault effects, it is seen that the SSI increases amplitude and stresses. Overall from the comparisons, the study indicates that the far-fault motion could be employed together with the near-fault motions for assessment of such historical mosques for further considerations.