A fuel cell system includes a raw fuel supply channel. A raw fuel supply apparatus, a desulfurizer, and a flow rate meter are provided in the raw fuel supply channel such that the desulfurizer is provided downstream of the raw fuel supply apparatus, and the flow rate meter is provided downstream of the desulfurizer. The raw fuel supply channel includes a first channel area provided upstream of the raw fuel supply apparatus, a second channel area provided downstream of the raw fuel supply apparatus, and upstream of the flow rate meter, a bypass channel having both ends connected to the first channel area and the second channel area, and an open/close valve for opening and closing the bypass channel based on the pressure in the first channel area and the pressure in the second channel area.