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As decarbonisation of the power sector is essential to achieve Japan’s target of net-zero greenhouse gas (GHG) emissions by 2050, it becomes crucial to address how the electricity system incorporates short- and long-term variability in the power output via renewable energy. In this paper, we developed six scenarios for 100% renewable energy in Japan’s power sector and conducted electricity system simulations of least-cost security-constrained unit commitment (SCUC) and security-constrained economic dispatch (SCED) of generators with capacity constraints for high-voltage transmission lines. The electricity demand under all scenarios assumed a drastic increase in electrification in all sectors and the use of hydrogen in areas where electrification is difficult. Regarding the electricity system, we assumed the use of the existing capacity of transmission lines with minor reinforcement in response to electrification and cross-regional coordination but not to renewable energy expansion. The results indicated that the domestic renewable energy share in the power mix can be increased to 100% within the constraints of the top two high-voltage transmission lines while maintaining the curtailment rate of renewable energy below 5% if hydrogen is produced using surplus renewable energy for power-to-gas (P2G) technology. It will become important to secure long-term flexibility for energy storage in large quantities across seasons, such as hydrogen-fired power plants with underground hydrogen storage. It was also shown that Japan exhibits enough potential to store hydrogen, which can be used for hydrogen-fired power plants and energy-intensive industries.