Apparatus for controlling a temperature of a thermal exchange medium of a patient temperature control system, comprising: a user interface configured to establish a programmed protocol in response to user input, for each of a plurality of phases that are non-overlapping in time, said plurality of phases comprising at least a first phase and a second phase, wherein a target patient temperature is established in response to said user input for each of said plurality of phases, and wherein a set phase duration is established in response to said user input for at least the second phase; a controller configured to receive a sensor output signal of a measured patient temperature on an ongoing basis; the controller further configured to output a control signal to cause circulation of a fluid thermal exchange medium through one or a plurality of pads for contact thermal exchange with a patient; and the controller further configured to control automatically the temperature of the thermal exchange medium, based upon said programmed protocol, during each of said plurality of phases; and, for each of said plurality of phases, to compare said measured patient temperature to the target patient temperature for the phase, automatically terminate and initiate, respectively, the first phase and the second phase of said plurality of phases upon a determination by said comparing that said measured patient temperature has reached the target patient temperature for said first phase of said at least two successive phases, and automatically terminating the second phase of said plurality of phases upon expiration of the set phase duration for the second phase. a user interface configured to establish a programmed protocol in response to user input, for each of a plurality of phases that are non-overlapping in time, said plurality of phases comprising at least a first phase and a second phase, wherein a target patient temperature is established in response to said user input for each of said plurality of phases, and wherein a set phase duration is established in response to said user input for at least the second phase; a controller configured to receive a sensor output signal of a measured patient temperature on an ongoing basis; the controller further configured to output a control signal to cause circulation of a fluid thermal exchange medium through one or a plurality of pads for contact thermal exchange with a patient; and the controller further configured to control automatically the temperature of the thermal exchange medium, based upon said programmed protocol, during each of said plurality of phases; and, for each of said plurality of phases, to compare said measured patient temperature to the target patient temperature for the phase, automatically terminate and initiate, respectively, the first phase and the second phase of said plurality of phases upon a determination by said comparing that said measured patient temperature has reached the target patient temperature for said first phase of said at least two successive phases, and automatically terminating the second phase of said plurality of phases upon expiration of the set phase duration for the second phase. compare said measured patient temperature to the target patient temperature for the phase, automatically terminate and initiate, respectively, the first phase and the second phase of said plurality of phases upon a determination by said comparing that said measured patient temperature has reached the target patient temperature for said first phase of said at least two successive phases, and automatically terminating the second phase of said plurality of phases upon expiration of the set phase duration for the second phase.