A patient temperature control system 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 upon the programmed protocol during each of the phases. A plurality of programmed protocols may be established, wherein a selected protocol may be utilized for automated temperature control during patient thermal therapy. The protocol may include a target patient temperature and/or a set duration for one or more of the phase of thermal therapy. The protocol may be user-definable and modifiable during therapy. In a multiphase 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.