Innovative energy and environmental technologies have an important role in achieving carbon neutrality. However, uncertainties regarding the potential of these technologies still remain. For this reason, possible scenarios for such technologies must be developed to facilitate forward-looking decision-making on national energy strategies. This study investigated multiple scenarios of future energy systems in Japan to achieve net-zero CO2 emissions by 2050 using a MARKAL (MARKet ALlocation) energy model. Six cases were configured based on different assumptions of renewable and nuclear power, carbon capture and storage, and hydrogen import, and the CO2 emissions, primary energy supply, final energy consumption, and electricity generation were compared for the different cases. The scenario analysis results suggest that electric power systems in Japan should be fully decarbonized by 2040 in order to achieve carbon neutrality by 2050, implying that renewable power generation should be dominant in the decarbonized electricity sector in Japan. The results also indicate that total energy supply and consumption in 2050 will be between 14.9–15.7 and 9.6–10.2 EJ, respectively, and that 211–256 Mt of CO2 will need to be removed using advanced CO2 removal technologies. The results further imply that CO2 removal technologies will become necessary when industrial decarbonization is difficult. •We built six scenarios of future energy systems in Japan toward carbon neutrality.•We used a MARKet ALlocation (MARKAL) energy model.•Power sector must reduce CO2 to ∼0 by 2040 to achieve carbon neutrality by 2050.•Total energy supply and consumption in 2050 will be 14.9–15.7 and 9.6–10.2 EJ.•Using advanced CO2 removal technologies, 211–256 Mt of CO2 must be removed.