A Medical Device Application (MDA) operates on the mobile device to temporarily configure it into a known secure configuration for use as an external controller, and to prevent operation of the mobile device inconsistent with this function. In particular, the MDA operates to (1) disable or reconfigure hardware modules, and/or (2) terminate or suspend software tasks, that might corrupt operation of the mobile device as an external controller. The MDA can comprise an application ("app") that the patient can download onto his mobile device and run to initialize the mobile device into the known secure configuration. The MDA also preferably provides a graphical user interface to allow a user to communicate with the implantable medical device using the now-secure mobile device. After using the mobile device to communicate with the implantable medical device, the MDA can be exited and the mobile device returned to its original configuration.
