A fuel cell system of the present invention includes: a fuel cell (101); a gas passage through which an electric power generating gas used for electric power generation in the fuel cell (101) flows; a cooling water passage through which cooling water for cooling down the fuel cell (101) flows; a cooling water tank (106) disposed on the cooling water passage to store the cooling water; a humidifier having a moisture permeable membrane (61) and configured to carry out moisture exchange between the cooling water flowing through the cooling water passage and the electric power generating gas flowing through the gas passage via the moisture permeable membrane (61); and a pressure compensating gas supplier (110) configured to supply a pressure compensating gas to a specific section including the humidifier on the gas passage when a pressure in the gas passage lowers, and a water surface of the cooling water tank (106) is higher than an upper end of the moisture permeable membrane (61) of the humidifier.