A hydrogen generator comprises a reformer configured to generate a hydrogen-containing gas through a reforming reaction in an internal space thereof using a material gas and steam; a material gas supply passage through which the material gas is supplied to the reformer; a material gas supplier which is provided at the material gas supply passage to supply the material gas to the reformer; a first valve configured to open and close the material gas supply passage; an evaporator configured to generate a steam supplied to the reformer; a water supplier configured to supply water to the evaporator; a communicating passage for allowing the reformer to communicate with atmosphere; a second valve configured to open and close the communicating passage; and a controller configured to stop the material gas supplier and the water supplier and close the first valve and the second valve at shutdown of the hydrogen generator; and open the second valve prior to opening the first valve when the material gas supplier resumes supply of the material gas to the reformer after the shutdown.