In this study, seismic vulnerability assessment and seismic isolation retrofit of Bayburt Yakutiye Mosque is investigated. Bayburt Yakutiye Mosque was built in the early 19th century at about 30-meter distance to Coruh river in the center of Bayburt in Turkey. The walls of historical masonry structure were built with regional white and yellow stones and the domes of the mosque was built with masonry bricks. This study is completed in four basic phases. In first phase, experimental determination of the regional white stone used in the historical structure are investigated to determine mechanical properties as modulus of elasticity, poison ratio and compression strengths etc. The required information of the other materials such as masonry brick and the regional yellow stone are obtained from literature studies. In the second phase, three dimensional finite element model (FEM) of the historical masonry structure is prepared with 4738 shell elements and 24789 solid elements in SAP2000 software. In third phase, the vulnerability assessment of the historical mosque is researched under seismic loading such as Erzincan (13 March 1992), Kocaeli (17 August 1999) and Van (23 November 2011) earthquakes. In this phase, the locations where damage can occur are determined. In the final phase, rubber base isolators for seismic isolation retrofit is used in the macro model of historical masonry mosque to prevent the damage risk. The results of all analyses are comparatively evaluated in details and presented in tables and graphs. The results show that the application of rubber base isolators can prevent to occur the destructive effect of earthquakes.