The development of hydrogen infrastructure is important because its commercialization will help reduce carbon dioxide emissions significantly. The construction of hydrogen fueling stations will increase the demand for fuel cell vehicles. While the risk associated with various types of fueling stations has been assessed, and appropriate safety regulations have been proposed, there have been few studies on hydrogen fueling stations with on-site dehydrogenation systems that use methylcyclohexane (MCH). This is because such stations are very new. In particular, the thermal hazards associated with such systems must be analyzed because they could lead to equipment damage. The purpose of the present study was to identify the thermal hazards of such systems using various thermal analysis methods. Thermal analyses were performed while assuming spontaneous ignition and oxidation under normal and abnormal conditions, in order to identify the thermal hazards associated with the storage of MCH, toluene, and heat carriers in underground storage tanks as well as their use in the dehydrogenation reactor. In addition, the thermal safety of the tank and the reactor was estimated based on the results of the thermal analyses. It was found that the underground storage tanks for MCH and toluene have a lower thermal risk because the process conditions are mild, and the thermal hazards related to the chemicals are low. Further, in the case of the dehydrogenation reactor, the risk of the spontaneous ignition of the heat carrier is low under quasi-adiabatic conditions and moderate air ventilation, in case the heat carrier leaks from damaged piping and equipment. However, it is important to regularly inspect the reactor to prevent any issues that may arise from an exothermic reaction of the heat carrier.