A patient temperature control system and method are provided for automated temperature control according to a programmed protocol. In one aspect, at least one programmed protocol may be established for each of a plurality of patient thermal therapy phases. In turn, the temperature of a thermal exchange medium may be controlled, based at least in part, upon the programmed protocol, during each of the phases. In another aspect, a plurality of programmed protocols may be established, wherein a selected one of the protocols (e.g. selected by a user at a user interface) may be utilized for automated temperature control during patient thermal therapy. The protocol(s) may include a target patient temperature and/or a set duration for one or more of the phase of thermal therapy. Further, the protocol(s) may be user-definable and modifiable during therapy. In a multi-phase configuration, automatic termination and initiation of successive phases may be selectively established by a user, based on target patient temperature data and/or set duration data on a phase-specific basis.