A system and method for safely altering the function of an implanted pacemaker in a noninvasive manner includes an implantable programmable pacemaker and a non-implantable programming device. The pacemaker includes a pulse generator that generates stimulation pulses as controlled by a control program. The control program, and associated control parameters, are stored in an implantable memory included within the pacemaker. The pacemaker further includes a telemetry circuit that allows the control parameters to be selectively changed or altered from a location remote from the pacemaker (i.e., a non-implanted location). The programmer includes a telemetry head for establishing a telemetry link with the pacemaker's telemetry circuit. Once a telemetry link is established, the programmer may be selectively operated to download a new control program into the pacemaker memory, thereby replacing the old control program previously stored in the pacemaker memory. As the downloading of the new control program takes place (which may require several minutes), the pacemaker includes backup control circuits, or equivalent, for controlling the pulse generator so that stimulation pulses are provided, as needed, until the downloading operation has been successfully completed. In this manner, the control program of the implantable pacemaker is noninvasively updated without having to explant the pacemaker, and without having to cease operation of the pacemaker.