AbstractThis study presents a novel approach to analysing the Japanese energy system transition from a mostly fossil fuels‐based system as of today, to a sustainable renewable energy‐based system by 2050. This research uses a novel technology‐rich, multi‐regional, multi‐sectoral, and cost‐optimal energy system model for the analysis, describing pathways to achieving the Japanese climate neutrality vision by 2050 based on renewables in the most cost‐effective manner. The energy transition of Japan is analysed for both rapid and delayed defossilisation pathways, impact of demand sensitivity, and benefit of sustainable energy imports in the form of electricity from Russia and China or e‐fuels from countries like Australia. The results show that a self‐sufficient energy system is achievable; however, some sustainable energy imports in the form of electricity and e‐fuels can be beneficial in further reducing overall investments, relieve pressure to develop local renewable resources and improving energy system flexibility. In addition, this research highlights the critical advantage of a fully renewable pathway, sector coupling, and high electrification rates as the most cost‐efficient way of achieving the Japanese climate neutrality vision by 2050. The renewable pathway also delivers an energy system with high levels of efficiency gains through direct and indirect renewable electricity usage.