A method of controlling a fuel cell system includes circulating a coolant through a fuel cell circulation passage in which a fuel cell and a gas liquid separator are provided. A valve is controlled selectively to connect or disconnect the fuel cell circulation passage and an air conditioning equipment circulation passage in which an air conditioning mechanism is provided. The valve is maintained to connect the fuel cell circulation passage and the air conditioning equipment circulation passage to circulate the coolant through the air conditioning equipment circulation passage when it is determined that the coolant includes air bubbles more than or equal to the threshold amount, when the valve connects the fuel cell circulation passage and the air conditioning equipment circulation passage, and when a temperature of the fuel cell is higher than or equal to a threshold temperature even if the air conditioning mechanism stops.