We study Japan’s net-zero emissions target by 2050 in a multi-model framework, focusing on residual emissions and carbon dioxide removal (CDR). Four energy-economic and integrated assessment models show similar but stronger strategies for the net-zero target, compared to the previous, low-carbon policy target (80% emissions reduction). Results indicate that around 90% (inter-model median) of the current emissions are reduced through abatement, including improved energy efficiency and cleaner electricity and fuels. Models deploy new options such as CDR based on carbon capture and storage (CCS) (bioenergy with CCS and direct air carbon dioxide capture and storage) and hydrogen to achieve net zero. The scale of CCS-based CDR deployment reaches an inter-model median of 132Mt-CO2/yr. The median hydrogen share of final energy in 2050 increases from 0.79% to 6.9% between the low-carbon and net-zero scenarios. The CDR sensitivity analysis reveals that limiting the use of CDR significantly increases the mitigation costs for net zero. Achieving Japan’s net-zero goal will require exploring methods to reduce residual emissions, including demand-side solutions, and accelerating responsible CDR policies.