A fuel cell system including a fuel cell, an air compressor that supplies oxidant gas to the fuel cell, an upstream supply pipe provided with the air compressor, a downstream supply pipe connected to the upstream supply pipe and the fuel cell, an upstream discharge pipe connected to the fuel cell, a downstream discharge pipe connected to the upstream discharge pipe, a bypass pipe, a valve mechanism configured to be switchable between a supply state and a bypass state, and a controller configured to control the air compressor, the valve mechanism, and a power generation state of the fuel cell.