A hydrogen generator (100) includes: a reformer (1) configured to generate a hydrogen-containing gas by a reforming reaction using a material gas; a hydro-desulfurizer (2) configured to remove a sulfur compound in the material gas; a recycled gas passage (9) through which the hydrogen-containing gas added to the material gas before the material gas flows into the hydro-desulfurizer (2) flows; a first on-off valve (3) disposed on the recycled gas passage (9); a material gas passage through which the material gas supplied to the reformer (1) flows; a second on-off valve (5) disposed on a portion of the material gas passage, the portion being located downstream of a connection portion where the material gas passage and the recycled gas passage (9) are connected to each other; and a controller (6) configured to open the first on-off valve (3) after the generation stop of the hydrogen-containing gas to supply the material gas to the recycled gas passage (9), and the controller (6) closes the second on-off valve (5) when it opens the first on-off valve (3).