Provided is a fuel cell system including a fuel cell (20) having a catalyst layer inside and receiving a reaction gas to generate electricity; and a coolant system (73) for supplying a coolant to thefuel cell to control temperature of the fuel cell. A method for stopping operation of the fuel cell system is also disclosed. If the system is placed under a low temperature environment the fuel cellis frozen and restart is disabled. For this, conventionally, upon stop of the system, the coolant flow rate to the fuel cell is reduced to lower the cooling performance and operation of the fuel cellis continued to increase the temperature of the fuel cell. However, the control may be useless since this is performed regardless of the condition upon the next system start. In order to solve this problem, when the temperature of the fuel cell (20) upon the next system start is estimated to be equal to or below a predetermined temperature, the coolant supply is stopped upon system stop and the coolant supply is resumed after a predetermined time has elapsed.