A fuel cell system has a fuel cell body, a gas flow path for supplying and discharging a reactant gas to and from the fuel cell, a regulating component for regulating conditions of a gas flow in the gas flow path, and at least two systems of scavenging routes for scavenging a portion of the gas flow path. A first scavenging route is formed to include a fuel cell body, and a second scavenging route is formed to bypass the fuel cell body.