A method for operating a hydrogen generator includes producing a hydrogen-containing gas from a source gas fed from a hydrodesulfurizer and reforming water with a reformer; feeding part of the hydrogen-containing gas to the hydrodesulfurizer as a recycle gas, and removing a sulfur compound contained in the source gas with the hydrodesulfurizer; condensing water vapor contained in the recycle gas in a recycle-gas channel through which the recycle gas flows, and separating the resulting condensed water from the recycle-gas channel; and regulating the amount of reforming water fed to the reformer on the basis of the temperature of the reformer.