A proximity-based security mechanism can control access to the programming interface of an implanted medical device. The security mechanism prevents unauthorized remote access to the programming interface by hackers or other hostile individuals, securing the safety of the subject. The system also allows the subject or other responsible person to activate the programming interface when changes to the operation of the implanted medical device are needed. In one example, a security interface is operable to detect, while implanted in the subject, an activation signal produced in close proximity to the subject, and activate the programming interface in response to the activation signal so that the implantable medical device can receive the programming instructions. A proximity-based security mechanism can be a dedicated device, or can be implemented in a programmable computing device such as a smartphone or other mobile computing device.