A fuel cell system includes a fuel cell having a membrane, which is adapted to perform power generation by a chemical reaction of two reaction gases each supplied to one side of the membrane, reaction gas paths through which the two reaction gases flow, a purge device for purging at least one of the two reaction gases from the reaction gas paths, a monitoring device for monitoring a state of the fuel cell after stopping of the power generation in the fuel cell, and a control unit for controlling the purge device so as to carry out a purge operation when it is determined by the monitoring device that the state of the fuel cell is a predetermined state.