A method of driving a fuel cell system is disclosed. The method of driving the fuel cell system may include supplying water to a reformer by pressing a pump pipe to pressing members to move the pressing members in a first direction, stopping power generation including stopping a supply of fuel and oxidant to the reformer, and discharging water in the reformer by moving the pressing members in a second direction opposite to the first direction while pressing the pump pipe with the pressing members. A fuel cell system is also disclosed. The fuel cell system includes a reformer, a fuel cell stack and a water transferring pump. The water transferring pump includes pressing members and a pump pipe. The pump pipe is in fluid communication with a water transferring pipe.