This invention provides a fuel cell system which can render the distribution of water in an electrolyte membrane even without lowering the pressure of a fuel gas. A fuel cell system (1) comprises an electrolyte membrane (11), an oxidant electrode provided on one side of the electrolyte membrane (11), and a fuel electrode provided on the other side of the electrolyte membrane (11). An oxidant gas flow passage (14) for supplying an oxidant gas along the face of the oxidant electrode and a fuel gas flow passage (15) for supplying a fuel gas along the face of the fuel electrode are provided so that the flow direction of the oxidant gas faces the flow direction of the fuel gas. A control unit (50) conducts control so that, when the electrolyte membrane (11) is dry, the flow rate of the fuel gas which flows through the fuel gas flow passage (15) is increased.