A fuel cell system includes a fuel cell stack, a reaction gas supply portion, and a control unit. The control unit performs two stages of purging that are a first purging and a second purging in which the flow rate of the reaction gas is smaller than the flow rate of the reaction gas of the first purging, and provides a purging standby time between the first purging and the second purging, and in a case in which an operation mode of the fuel cell stack when power generation of the fuel cell stack is stopped is a high output mode in which an output is higher than the output of a normal mode, the control unit makes a purging time longer than the purging time of the first purging that is performed in the normal mode.