In order to provide a fuel cell system (which ensures high proton conductivity and high energy conversion efficiency and, in addition, copes with an operating mode of the startup/shutdown type and which has excellent durability capable of effectively preventing a polymer electrolyte membrane from deterioration) and an operating method of such a fuel cell system, a fuel cell system (100) is provided with a fuel cell (11), a fuel gas supplier (16) and an oxidizing gas supplier (17), a temperature supplier (19) which controls the temperature of the fuel cell, and a humidifier unit (18) which humidifies oxidizing gas, wherein there is further provided a controller (20) which controls the dew point of fuel gas and the dew point of oxidizing gas as follow: during the generation of electric power, the fuel gas dew point is made higher than or equal to the temperature of the fuel cell while the oxidizing gas dew point is made less than the temperature of the fuel cell and, before interrupting the electric connection between the fuel cell and a load, at least, the temperature of the fuel cell and the oxidizing gas dew point are made to conform to each other.