A fuel cell system includes a fuel cell stack configured to generate power according to a load, a fuel tank configured to store fuel gas, a pressure regulating valve configured to regulate a pressure of the fuel gas supplied from the fuel tank to the fuel cell stack, a purge valve configured to purge the fuel gas discharged from the fuel cell stack and a controller for controlling the system. The controller includes a pulsating unit configured to cause a fuel gas pressure of the fuel cell stack to pulsate, and a pressure increasing rate setting unit configured to set a pressure increasing rate of the pulsation of the fuel gas pressure according to an operating state.