Methods of operating a fuel cell and a power supply systems are provided. The methods and systems of the present invention are capable of suppressing condensation of moisture obstructing an air passage without the need of any complicated system configuration. The method of operating a fuel cell includes controlling a supply of air while monitoring a relative humidity of exhausted air. The step of controlling the supply of air can be performed such that the relative humidity of exhausted air becomes equal to or less than a specific humidity. The power supply system including, as a power supply, a fuel cell having an air supply unit, an air exhaust unit, and a fuel gas supply unit includes a humidity sensor provided on the air exhaust unit, and a control mechanism for controlling a supplied amount of air in the air supply unit based on the information provided from the humidity sensor.