A system and method for facilitating bi-directional authentication between an external device and an implanted medical device (IMD), wherein a therapy application executing on the external device is operative to communicate with the IMD via wireless telemetry communications. Certified security credentials for respective devices may be provisioned with respect to the therapy application. Upon initiating wireless telemetry communications, respective certified security credentials are mutually verified by the external device and the IMD. Responsive to successful verification, a mutual authentication process may be executed between the external device and the IMD using a respective challenge-response sequence.