Nuclear power plants are required to maintain operation after an earthquake, leading to a safe shutdown if necessary. In the case of a loss of offsite power, the onsite emergency diesel generator is critical to ensure procedural operations of the nuclear power plant. As a means to reduce the overall seismic risk, a three-dimensional seismic protection system is proposed to enhance the seismic performance of the emergency diesel generator. The proposed seismic isolation system decouples the horizontal and vertical components of shaking and considers available hardware to achieve an effective isolation solution over the range of excitation frequencies considered. Numerical analysis of the proposed system demonstrates a reduction in seismic demands on the emergency diesel generator and provides a higher safety margin than conventional base installation procedures. Umbilical lines that cross the isolation plane are considered and impose additional constraints on the displacement capacity of the isolation system. However, increasing the displacement capacity of these components can significantly increase the safety margin against failure. The seismic protection system can be customized depending on the seismic hazard and application to different seismic regions.