A fuel cell system includes first and second fuel cells each generating electric power using fuel gas and oxidant gas, first and second fuel gas supply devices supplying the fuel gas, first and second circulation paths circulating the discharged fuel gas to the first and second fuel cells, a communication path communicated with the first and second circulation paths, an opening/closing device causing the first and second circulation path to be communicated or to be disconnected by opening/closing the communication path, and a controller configured to determine whether there is a possibility of flooding, and when determining that there is the possibility of flooding, suspend power generation of one of the first and second fuel cells while maintaining supply of the fuel gas, and cause the opening/closing device to make the first and second circulation paths be communicated with each other.