A fuel cell system comprising: a hydro-desulfurizer configured to cause a sulfur compound in a material gas to react with hydrogen to remove the sulfur compound; a material supply unit configured to boost the material gas to supply the material gas to the hydro-desulfurizer; a hydrogen generator configured to cause a reaction between the material gas having flowed through the hydro-desulfurizer and steam to generate a hydrogen-containing fuel gas; a fuel cell configured to generate electric power using the fuel gas discharged from the hydrogen generator and an oxidizing gas; a fuel gas channel through which the fuel gas discharged from the hydrogen generator is supplied to the fuel cell; a recycled gas channel which branches from a branching portion of the fuel gas channel and by which a part of the fuel gas discharged from the hydrogen generator is mixed with the material gas before the material gas flows into the material supply unit; an off fuel gas channel through which a hydrogen-containing off fuel gas unconsumed by the fuel cell is discharged from the fuel cell; a first on-off valve; a clogging detector configured to detect clogging of the recycled gas channel; and a controller, wherein the clogging detector is selected from the group consisting of a pressure detector, a temperature detector and a flow rate detector, and the controller is configured to close the first on-off valve and activate the material supply unit when the clogging detector detects the clogging, characterized in that the first on-off valve is disposed at at least one of the fuel gas channel provided downstream of the branching portion and the off fuel gas channel. a hydro-desulfurizer configured to cause a sulfur compound in a material gas to react with hydrogen to remove the sulfur compound; a material supply unit configured to boost the material gas to supply the material gas to the hydro-desulfurizer; a hydrogen generator configured to cause a reaction between the material gas having flowed through the hydro-desulfurizer and steam to generate a hydrogen-containing fuel gas; a fuel cell configured to generate electric power using the fuel gas discharged from the hydrogen generator and an oxidizing gas; a fuel gas channel through which the fuel gas discharged from the hydrogen generator is supplied to the fuel cell; a recycled gas channel which branches from a branching portion of the fuel gas channel and by which a part of the fuel gas discharged from the hydrogen generator is mixed with the material gas before the material gas flows into the material supply unit; an off fuel gas channel through which a hydrogen-containing off fuel gas unconsumed by the fuel cell is discharged from the fuel cell; a first on-off valve; a clogging detector configured to detect clogging of the recycled gas channel; and a controller, wherein the clogging detector is selected from the group consisting of a pressure detector, a temperature detector and a flow rate detector, and the controller is configured to close the first on-off valve and activate the material supply unit when the clogging detector detects the clogging, characterized in that the first on-off valve is disposed at at least one of the fuel gas channel provided downstream of the branching portion and the off fuel gas channel.