A method for purging a fuel cell system comprises detecting a signal for stopping an operation of a fuel cell system, cutting off an electricity output of the fuel cell system, driving a steam generator of a fuel supply unit of the fuel cell system for a certain time and thereby generating steam, certifying whether a purging operation of the fuel cell system has been completed or not, and stopping the fuel cell system, in which the fuel cell system is purged by using steam generated by the steam generator. Since an additional container for storing nitrogen is not required, a fabrication cost is reduced. Also, inconvenience caused by periodically containing nitrogen in the container is solved. Furthermore, when the fuel cell system is used at home, an additional space for installing the nitrogen container is not required and the fuel cell system can be easily installed.