A fuel cell system and a method for operating the same are disclosed. In one embodiment, a fuel cell system includes a fuel supplier, a reformer for reforming a fuel supplied from the fuel supplier into hydrogen gas by a reforming reaction, and a fuel cell stack for generating electrical energy by an electrochemical reaction between the hydrogen gas and an oxidizing agent. When the fuel cell system is to be stopped, the reforming reaction of the reformer and the electrochemical reaction of the fuel cell are stopped and a portion of unreformed fuel is fed to the reformer and the fuel cell stack. Residual hydrogen is reacted and residual power from the fuel cell stack is dissipated by a power dissipation circuit. By largely removing hydrogen from the fuel cell stack on a stopped condition, reactions that are detrimental to the fuel cell membrane are reduced.