A fuel cell system includes a fuel cell which generates electrical energy by reacting a hydrogen gas from a hydrogen gas supply source and an oxidizing agent gas from an oxidizing agent gas supply source, a hydrogen circulating pump which is provided in a hydrogen circulation path and transfers hydrogen gas of the hydrogen circulation path to the fuel cell, and control means. When the supply of hydrogen gas from the hydrogen gas supply source to the fuel cell is discontinued, the control means discontinues the supply of oxidizing agent gas from the oxidizing agent gas supply source to the fuel cell and activates the hydrogen circulating pump such that electrical energy generated in the fuel cell is supplied to the hydrogen circulating pump.