The disclosure concerns a computer-controlled system for interval thermal therapy; the system including a control unit console configured for placement on a bench-top or similar setup, the console is connected to a hand-held thermal therapy application assembly, either by way of a cable extending between the hand-held assembly and the console, or via a cordless coupling therebetween. The hand-held assembly generally comprises a removeably applicator with a thermally conductive contact surface configured to communicate hot or cold thermal energy, or a combination of hot and cold thermal therapy in various intervals, the contact surface of the hand held assembly is used to contact a patient's body at a desired treatment site for effectuating various physiological treatments or therapies.