The fuel cell system of the present disclosure includes: a fuel cell that includes a membrane electrode assembly including a proton conducting ceramic electrolyte membrane, a cathode disposed on a first surface of the electrolyte membrane, and an anode disposed on a second surface of the electrolyte membrane, the fuel cell generating electric power through an electrochemical reaction using a fuel gas and an oxidant gas; a power source that applies a voltage to the fuel cell; and a controller. In a shutdown process, the controller controls the power source to apply the voltage to the fuel cell such that a terminal voltage of the fuel cell is equal to or higher than an open circuit voltage of the fuel cell.