To provide a fuel cell system capable of starting with safety even without the use of purge gas such as nitrogen gas, and capable of preventing deterioration of performance accompanying starting and shutdown.

The fuel cell system, composed of a fuel cell stack made by laminating the given number of unit cells each consisting of two sheets of gas diffusion electrodes pinching a solid polymer electrolyte film, and a separator having a fuel gas distribution channel, an oxidant gas distribution channel, and a water disrtibution channel, a fuel gas supply means, an oxidant gas supply means, and a cooling water supply means, is provided with a cooling water exhaust means exhausting cooling water from the fuel cell stack by a cooling water pump, a cooling water buffer between the cooling water pump and the fuel cell stack. The cooling water buffer is set at a position higher than the fuel cell stack, so that supply of the fuel gas or the oxidant gas is stopped as well as the cooling water pump is stopped at the shutdown of operation of the fuel cell system, and water in the cooling water buffer is supplied to either the fuel gas distribution channel or the oxidant gas distribution channel through a conductive porous material.

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