A fuel cell system and a method of operating the same is provided that is capable of reducing degradation of a cathode catalyst of a fuel cell. A fuel cell system is provided that includes a fuel cell having a catalyst used for an anode, wherein a carrier of the catalyst is composed of a material with a property where electric resistance in an oxygen containing atmosphere is greater than electric resistance in a hydrogen atmosphere; and a control device configured to control the fuel cell, when supply of fuel gas is stopped during stoppage of operation of the fuel cell, to consume all or part of the fuel gas in a fuel gas chamber, followed by introducing oxygen containing gas into the fuel gas chamber.