A method of operating a fuel cell system, the fuel cell system including: a fuel cell configured to generate electric power by causing a fuel gas and an oxidizing gas to react with each other; a reformer configured to generate the fuel gas by reforming a raw material, and supply the fuel gas to the fuel cell; a combustor configured to combust a combustible gas to heat the reformer, a casing accommodating at least the fuel cell, the casing including an air inlet and an exhaust outlet formed therein; a supply passage connected to the air inlet, the supply passage being configured to introduce external air into the casing from outside of the casing; an exhaust passage connected to the exhaust outlet, the exhaust passage being configured to exchange heat with the supply passage and discharge at least air inside the casing to the outside of the casing, the exhaust passage is in communication with the combustor in such a manner as to discharge a flue gas from the combustor; and an air supply device configured to introduce the external air into the casing through the supply passage, the air supply device includes a ventilator configured to ventilate the air inside the casing, and a combustion air supply device configured to supply combustion air to the combustor, the method comprising: step 1 of determining, after having caused the air supply device to operate, whether or not at least one of a temperature inside the casing, a temperature of the supply passage, and a temperature of the exhaust passage is lower than or equal to a first predetermined temperature; step 2 of reducing an amount of air supplied by the air supply device and causing the air supply device to continue operating if at least one of the temperatures is lower than or equal to the first predetermined temperature; and if the temperature, after causing the air supply device to operate, is lower than or equal to a second predetermined temperature, which is lower than the first predetermined temperature, the method comprising step 3 of causing the ventilator to stop operating, causing the combustion air supply device to operate, and causing the combustor to perform combustion. a fuel cell configured to generate electric power by causing a fuel gas and an oxidizing gas to react with each other; a reformer configured to generate the fuel gas by reforming a raw material, and supply the fuel gas to the fuel cell; a combustor configured to combust a combustible gas to heat the reformer, a casing accommodating at least the fuel cell, the casing including an air inlet and an exhaust outlet formed therein; a supply passage connected to the air inlet, the supply passage being configured to introduce external air into the casing from outside of the casing; an exhaust passage connected to the exhaust outlet, the exhaust passage being configured to exchange heat with the supply passage and discharge at least air inside the casing to the outside of the casing, the exhaust passage is in communication with the combustor in such a manner as to discharge a flue gas from the combustor; and an air supply device configured to introduce the external air into the casing through the supply passage, the air supply device includes a ventilator configured to ventilate the air inside the casing, and a combustion air supply device configured to supply combustion air to the combustor, step 1 of determining, after having caused the air supply device to operate, whether or not at least one of a temperature inside the casing, a temperature of the supply passage, and a temperature of the exhaust passage is lower than or equal to a first predetermined temperature; step 2 of reducing an amount of air supplied by the air supply device and causing the air supply device to continue operating if at least one of the temperatures is lower than or equal to the first predetermined temperature; and if the temperature, after causing the air supply device to operate, is lower than or equal to a second predetermined temperature, which is lower than the first predetermined temperature, the method comprising step 3 of causing the ventilator to stop operating, causing the combustion air supply device to operate, and causing the combustor to perform combustion.