After the severe accident at the Fukushima-Daiichi nuclear power station, the regulation of nuclear plant safety in Japan was upgraded, and continuous effort to enhance risk management in the medium and long term is required. Seismic risk is important in Japan, and one of the major issues of current probabilistic risk assessment (PRA) methodology is the enhancement of seismic PRA including the evaluation of initiating events induced by simultaneous multiple failures of components and of subsequent accident sequences. The Nuclear Regulation Authority (NRA) addressed the issue as “…multiple-failure-initiating events should be considered.” In addition, the standard for the procedure of seismic PRA for nuclear power plants in 2015 identifies this issue in the same manner. This study proposes an enhanced seismic PRA methodology considering multiple-failure-initiating events that is expected to contribute to improving the safety of nuclear power plants. This study also discusses the issues that need more research for their resolution.