A reformer of a fuel cell system includes a heat source unit for generating heat, a reforming reaction unit for generating a reforming gas containing hydrogen from a fuel through a fuel reforming reaction using the heat, a carbon monoxide reducing unit connected to a reforming reaction unit to reduce a concentration of carbon monoxide contained in the reforming gas, and a thermal treatment unit disposed outside the reforming reaction unit and the carbon monoxide reducing unit to adjust the thermal energy supplied to the reforming reaction unit and the carbon monoxide reducing unit.