There is provided a fuel cell system comprising: a reformer for generating a hydrogen gas stream from fuel through a catalytic chemical reaction using thermal energy; and a stack for generating electric energy through a reaction between the hydrogen gas stream and oxygen. The reformer includes: a first reaction section for generating thermal energy through an oxidation reaction of fuel during start-up of the fuel cell system; a second reaction section which communicates with the first reaction section and which generates the hydrogen gas stream from the fuel through a reforming reaction using the thermal energy; and a third reaction section which communicates with the first and second reaction sections, and which generates thermal energy through an oxidation reaction of carbon monoxide contained in the hydrogen gas stream, thereby reducing the concentration of carbon monoxide in the hydrogen gas stream.