A system and method for adding or removing heat from a heat exchange fluid circulating between an external heat exchanger and an intravascular heat exchange catheter is described. The system includes a two stage cooling system providing for a high rate of cooling in one stage and a lower rate of cooling in a second stage. Both stages may be used to provide maximal cooling while the second stage is used to provide improved control of the cooling rate as a target temperature is approached. The second stage may also be used to provide heat to the heat exchange fluid.