A fuel cell system of controlling a valve assembly to maintain a feed flow rate while avoiding a vibration generation range in order to reduce noise due to vibrations generated in the valve assembly is provided. The fuel cell system includes a fuel cell stack that receives fuel and generates electric energy and a valve assembly that adjusts a flow rate of fuel that is supplied to the fuel cell stack. A controller then oscillates the flow rate of the fuel to alternately have a first value that is equal to or greater than a upper limit value of a first vibration generation range and a second value that is equal to or less than a lower limit value of the first vibration generation range, in response to determining that the flow rate of the fuel supplied through the valve assembly is included in the first vibration generation range.