Over-track buildings require seismic performance enhancement as well as minimization of the vibration propagated by trains running below them. To this end, we have proposed a structural system for a building with functions to isolate both seismic and vibration effects. In this system, laminated rubber bearings that are softer in the vertical direction than general ones are set into the middle story of the building. Through response analysis, this study demonstrates a high level of seismic performance, and the reduction of train-induced vibration is confirmed using model experiments and numerical analysis.