A vehicle includes a traction battery having a plurality of cells arranged in arrays and grouped into a plurality of cooling zones. A thermal management system includes a plurality of distinct circuits each associated with one of the zones. The thermal management system is configured to provide individual heating or cooling to each of the circuits to independently control temperatures of the zones. A controller is programmed to, in response to one of the zones exceeding a first threshold temperature and another of the zones being less a second threshold temperature, command the thermal management system to provide cooling to the circuit associated with the one of the zones and command the thermal management system to provide heating to the circuit associated with the another of the zones.