A hydrogen generator has: a reformer that produces hydrogen-containing gas from raw material gas through reforming; a temperature detector that detects the temperature of the reformer; a hydro-desulfurizer that removes sulfur from the raw material gas through hydrodesulfurization; a recycle flow passage through which recycle gas as a portion of the hydrogen-containing gas is supplied to the hydro-desulfurizer; a raw material gas flow detector that detects the flow rate of the raw material gas, the raw material gas flow detector located somewhere in a flow passage for the raw material gas upstream of a junction of the recycle gas and the raw material gas; and a controller that controls the flow rate of the recycle gas in accordance with the temperature of the reformer, the flow rate of the raw material gas, and the flow rate of the recycle gas.