Various low-carbon technologies, including hydrogen utilization, should have functional roles in decarbonizing the future energy systems. However, each low-carbon technology has some level of uncertainty associated with its development and implementation, which can affect the long-term energy transition of an economy. Multiple possible scenarios for low-carbon technologies should be considered to make flexible decisions given these uncertainties. In this study, we aim to clarify the role of hydrogen in the future energy system of Japan using a MARKet ALlocation (MARKAL) model developed by the AIST. The transition of the energy system of Japan is simulated under various settings for low-carbon technologies such as renewable power generation. From the MARKAL simulation, we compare CO2 emissions, primary energy supplies, and electricity generation by 2050 under different technological development settings.