A fuel cell system which includes: a fuel cell having a fuel gas flow path and an oxidant gas flow path and generating electricity by being supplied a fuel gas to the fuel gas flow path and an oxidant gas to the oxidant gas flow path; fuel gas supplying means; a discharge valve; fuel gas exchange means for exchanging an atmosphere inside the fuel gas flow path for the fuel gas at a starting of the system; and cold start determination means for determining whether to conduct or not to conduct the cold start of the system, wherein when the cold start determination means determines to conduct the cold start, the cold start determination means increases a total discharge amount of a gas to be discharged for exchanging the atmosphere inside the fuel gas flow path for the fuel gas, and thereby increases a fuel gas concentration in the fuel gas flow path.