A control device for a fuel cell system (2) having a fuel cell stack (11) with an oxidizing electrode (11b) supplied with oxidizing gas and a fuel electrode (11a) supplied with fuel gas to generate an electric power is disclosed having an estimating section (13) estimating occurrence of a water-clogging phenomenon wherein condensed water stays in a fuel gas flow passage (HL, HL') through which fuel gas is supplied to the fuel electrode of the fuel cell stack, and a control section (14) controlling a fuel gas exhaust valve (15), which is disposed downstream of the fuel cell stack to allow the fuel gas to be exhausted from the fuel cell stack, to be brought into an opened condition when the estimating section estimates the occurrence of the water-clogging phenomenon.