A multiple fuel cell thermal management system controls a proportional mixing valve, heat exchanger bypass valves, fan speeds, and pump speeds of respective coolant circuits and associated fuel-cell stacks to operate the stacks independently or in combination. When vehicle wheel loads are low or in applications with standby fuel-cell stacks, selected stacks are turned off. During moderate loads or high ambient temperature, the working fuel cell cooling system(s) operates in parasitic load reduction mode, using the non-working cooling circuit(s) as a heat sink running the associated pump at low speed and throttling the proportional mixing valve such that efficient cooling is accomplished in the running circuit with less fan power required than if the non-working circuit is completely shut down. A heat exchanger bypass valve and fan speed are controlled to provide a target stack inlet temperature. Pump speed is controlled responsive to a stack inlet/outlet temperature difference.