A fuel cell system for a hybrid vehicle that includes a high voltage battery, where the system uses a cathode exhaust gas airflow from a fuel cell stack to draw air through a battery compartment in which the battery is mounted to provide battery cooling. An air intake line is in fluid communication with the passenger compartment of the vehicle and the battery compartment. An ejector line is in fluid communication with the battery compartment and the cathode exhaust gas pipe. The flow of the cathode exhaust gas around the injector pipe creates a low pressure area, which draws air through the battery compartment from the passenger compartment. In one embodiment, a compressor that provides the cathode inlet air to the fuel cell stack is used at low stack output loads, such as during vehicle idle, to direct air through the cathode exhaust gas pipe, and cool the battery system under low load conditions.