To provide an operation method of a fuel cell system which even when the fuel cell repeats stop and start, can avoid degradation of the fuel cell and a fuel cell system for carrying out the method. An operation method of a fuel cell system which is provided with a fuel cell having at least one cell provided with an electrolyte, an anode and a cathode each having a platinum based metallic catalyst, the electrolyte being put between the anode and the cathode, and a pair of separator plates having formed thereon gas passages for feeding a fuel gas into the anode and feeding an oxidizing agent gas into the cathode, respectively and which switches connection and disconnection between the fuel cell and a load, wherein feeding of the oxidizing agent gas into the cathode and feeding of the fuel gas into the anode are continued until a prescribed period of time elapses after disconnection between the fuel cell and the load, and thereafter, feeding of each of the oxidizing agent gas and the fuel gas is stopped, thereby controlling the operation such that the time when the cell of the fuel cell has a voltage of 0.9 V or more falls within 10 minutes.