A hydrogen generator includes: a desulfurizer including a desulfurization catalyst that removes a sulfur compound in a raw material by a desulfurization reaction, the desulfurization catalyst being arranged so as to be heated by a first heat source; a reformer configured to generate a hydrogen-containing gas using the raw material having flowed through the desulfurizer; a first temperature detector configured to detect a temperature of a predetermined portion of the desulfurization catalyst; a second temperature detector configured to detect the temperature of a portion of the desulfurization catalyst, the portion being located such that a distance between the portion and the first heat source is longer than a distance between the predetermined portion and the first heat source; and a controller configured to control an operation of heating the desulfurization catalyst by the first heat source, based on detection results of the first temperature detector and the second temperature detector.