A fuel cell system includes a fuel cell stack including an air electrode and a fuel electrode, a stack housing having a hollow therein to accommodate the fuel cell stack in the hollow, an air compressor configured to pump air to supply the air to the air electrode, a ventilation pipe connecting an entrance of the air compressor and the hollow, and at least one vent hole provided on an outer wall of the stack housing such that the hollow and an outside of the stack housing communicate with each other. An interior of the stack housing is ventilated by lowering of a pressure at the entrance of the air compressor, which is generated as the air compressor is operated, while air outside the stack housing is suctioned into the entrance of the air compressor after passing through the vent hole, the hollow, and the ventilation pipe.