CO2 emissions associated with hydrogen production can be reduced replacing steam methane reforming with electrolysis using renewable electricity with a trade-off of increasing energy consumption, water consumption and cost. In this research, a linear programming optimization model of a hydrogen production system that considers simultaneously energy consumption, water consumption, CO2 emissions and cost on a cradle-to-gate basis was developed. The model was used to evaluate the impact of CO2 intensity on the optimum design of a hydrogen production system for Japan considering different stakeholders’ priorities. Hydrogen is produced using steam methane reforming and electrolysis. Electricity sources include grid, wind, solar photovoltaic, geothermal and hydro. Independent of the stakeholders’ priorities, steam methane reforming dominates hydrogen production for cradle-to-gate CO2 intensities larger than 9 kg CO2/kg H2, while electrolysis using renewable electricity dominates for lower cradle-to-gate CO2 intensities. Reducing the cradle-to-gate CO2 intensity increases energy consumption, water consumption and specific cost of hydrogen production. For a cradle-to-gate CO2 intensity of 0 kg CO2/kg H2, the specific cost of hydrogen production varies between 8.81 and 13.6 USD/kg H2; higher than the specific cost of hydrogen production targeted by the Japanese government in 2030 of 30 JPY/Nm3, 3.19 USD/kg H2.