A fuel cell system includes a stack for generating electrical energy through electrochemical reaction between a fuel and oxygen and supplying the electrical energy to a load, a fuel supply unit for supplying the fuel to the stack, an oxygen supply unit for supplying the oxygen to the stack, and a comparator coupled to the stack to compare an electricity output value of the stack with a reference electricity output value corresponding to the load and to selectively electrically connect the stack to the load according to the electricity output value.