A fuel cell system includes a fuel cell stack, a reformer which generates a reformed gas through a reforming reaction between a gaseous fuel and water and supplies the reformed gas to the fuel cell stack, a fuel tank which compresses the gaseous fuel, stores the compressed fuel in an at least a partially liquid phase, and supplies the gaseous fuel to the reformer, a water tank connected to the fuel tank and the reformer to store water and to supply the water to the reformer by an internal air pressure of the fuel tank, and a first valve installed in a connection line connecting the water tank to the fuel tank to selectively open or close the connection line according to an electrical on/off pulse signal.