To provide a fuel cell system configured to increase fuel cell performance even at high altitude. A fuel cell system for air vehicles, wherein the fuel cell system comprises: a fuel cell, an oxidant gas system for supplying oxidant gas to the fuel cell, an altitude sensor, and a controller; wherein the oxidant gas system comprises an air compressor and a bypass flow path bypassing the fuel cell; wherein the bypass flow path comprises a bypass valve; and wherein, when the controller detects an altitude increase measured by the altitude sensor, the controller increases a rotational speed of the air compressor, and the controller increases an opening degree of the bypass valve.