Abstract Japanese energy system toward the mid-century has been assessed using an energy system model with inter-temporal optimization of total system cost, TIMES-Japan. The assessment framework couples the energy system model and detail sectoral models such as power system model, wind and solar power capacity potential models, and building energy model via soft-linkage. 70%, 80% and 90% emissions reductions targets at 2050 are assessed with varying assumption of carbon capture and storage (CCS) and nuclear power. It shows sensitivity in the final energy consumption of zero emissions carriers in transportation sector, particularly in LDV. Availability of power generation using biomass with CCS (BECCS) is also considered in the model to evaluate transitions of energy systems toward net-zero emissions after 2050.