The U.S. Nuclear Regulatory Commission’s functional containment concept provides advanced nuclear power plant designers with more flexibility in terms of the civil/structural design if the appropriate set of barriers for prevention of radioactive material release exist. Some of the conceptual advanced reactor structures, without the traditional pressure boundaries of large containment structures, are proposed to be deeply embedded or buried into soil. This approach is expected to provide (1) lesser seismic demands on the structures and safety-critical structures, (2) eased regulatory efforts and overall design against other external hazards such as aircraft impact, and (3) overall cost savings. One of the important aspects of assessing the technical and economic viability of deeply embedding advanced reactor buildings is to assess the seismic performance with the understanding of effects with material and geometric nonlinearities. This study investigates the seismic response of deeply embedded or buried advanced reactors by conducting three-dimensional nonlinear soil-structure interaction analyses. Although the results indicate that there is a general trend of decreased seismic response with increased embedment depths, the change in the dynamic environment with different embedment depths and the nonlinear environment under high-intensity seismic inputs may result in increased peak response at increased embedment depths.