A design algorithm is proposed for locally minimizing the structural cost of seismically isolated buildings. The design variables are the types and sizes of isolation devices, and the section sizes and reinforcement ratios in RC members in the superstructure. The design constraints are defined for the multiple properties evaluated in the response history analyses such as the lateral displacements and story shear coefficients. The effectiveness of the algorithm is verified in application to a seismically isolated building with a 21-story RC frame superstructure. A design possibility to reduce the cost in both the isolation layer and superstructure is demonstrated.