The disclosure relates to an electrical trial stimulator that stores multiple applications to selectively emulate the operation of different chronically implanted stimulators. Each application corresponds to a different chronically implanted stimulator. Upon selection of a particular application, the stimulator executes a set of instructions to emulate the operation of a chronically implanted stimulator that corresponds to the application. The multi-application stimulator permits a physician to select an application for stimulation therapy, and evaluate efficacy of a particular chronically implanted stimulator. In addition, the physician may select any of the other stimulation applications to emulate other stimulators. The different stimulation applications may correspond to different stimulators that deliver a similar therapy, e.g., stimulators designed to deliver spinal cord stimulation for alleviation of chronic pain. Alternatively, the applications may correspond to stimulators that deliver different types of therapy, e.g., stimulators that deliver spinal cord, deep brain, gastrointestinal, or pelvic floor stimulation.