Before warmup of a fuel cell stack (1) is complete, a cooling water pressure of the fuel cell stack (1) is suppressed lower than the pressure used when the fuel cell system is run in the steady state. In this way, when the system is started from a low temperature state, water in a cathode (2) and anode (3) flows efficiently into the cooling water passage (9), and water clogging is prevented while maintaining a proper water balance in the fuel cell system.