A fuel cell system is provided, the system comprising: a fuel cell (1) configured to generate electric power by use of a fuel gas; a reformer (2) configured to generate the fuel gas by reforming a raw material; a combustion burner (2a) configured to supply heat for reforming; a raw material feeder (10) configured to control the feed rate of combustion fuel to the combustion burner; a combustion fan (2b) configured to supply air to the combustion burner; a fuel gas passage (R1, R4); an off gas passage (R3, R5); a bypass passage (R2); a switching valve (8); and a controller (101), wherein the inside of the fuel cell is filled with the raw material before the fuel gas is supplied, and wherein the controller controls the raw material feeder so as to reduce the feed rate of the combustion fuel to the combustion burner when controlling the switching valve so as to shut off the bypass passage to supply the fuel gas generated in the reformer to the fuel cell. This fuel cell system is environmentally-friendly and capable of suppressing the emission of carbon monoxide at the start of a power generating operation to mitigate the adverse effect upon the ecosystem.