In a hydrogen generator according to the invention, a reformer temperature sensor detects the temperature of a reformer at a start of a stop operation of a hydrogen generator. In a controller, a processing and controlling portion compares the detected temperature with first to fourth reference temperatures pre-stored in a storage portion, and determines which of the following conditions is the temperature condition of the hydrogen generator at the stop; a first condition in which water condensation occurs, a second condition in which water condensation and carbon deposition are avoidable, a third condition in which carbon deposition occurs, a fourth condition in which disproportionation reaction occurs, and a fifth condition in which oxidization of catalyst occurs. According to the determination result, an appropriate setting is selected among first to fifth replacement settings pre-stored in the controller corresponding to the first to fifth conditions, and an internal gas replacement operation is performed according to the selected setting.