A flush and fill process is used to ready a fuel cell cooling circuit for initial use. An external flushing system releasably connected to the cooling circuit circulates flushing coolant through the cooling circuit to remove contaminants from the wetted surfaces of the cooling circuit before the fuel cell is put into use. The flushing system includes a pump for circulating the flushing coolant through the cooling circuit, filters for removing contaminants from the coolant and a heater for elevating the temperature of the coolant. Following the flushing process to remove contaminants, the flushing system is disconnected from the cooling circuit and the cooling circuit is filled with fresh coolant.