The study of earthquake resistance design on cyclotron bunkers using base isolators was introduced. With the increasing trend of detection and treatment of cancer using nuclear technology in Indonesia, the construction of nuclear medicine facilities which include the manufacture of radiopharmaceuticals using a cyclotron facility must be held immediately. With the many areas in Indonesia in earthquake-prone areas, a cyclotron bunker design is needed that can accommodate the effects of the earthquake. The cyclotron bunker must be able to withstand earthquake loads without damage because apart from being a building structure, concrete also acts as shielding radiation during cyclotron operations. Base isolators have become a reliable technology in overcoming earthquake loads and will be used in cyclotron buildings in earthquake areas. By using the spectrum response method in the cyclotron building, the results of the base isolator will be evaluated. It was found that building acceleration after adding base isolators decreased 37% and base isolators also increased the vibration period of cyclotron bunkers away from the earthquake period.