COVID-19 pandemic has spread very fast across the world. This has been a surprise to everyone and shown how unprepared the world was for such a pandemic. Tracking the host carrying the virus has been one of the major issues during this pandemic. Many potential solutions were proposed for tracking the host but the privacy and security of the people being tracked are at stake in this case. This article proposes physical unclonable function (PUF)-based privacy-aware identification module, an Internet-of-Medical-Things (IoMT) architecture to track the host carrying the virus in a crowded area. The privacy and security of the host or the person carrying the IoMT device is given the highest priority and the data being transmitted do not contain any data related to the person carrying the device. A new multikey PUF architecture is also proposed in this article to generate unique identification keys for the proposed protocol. The average time taken to generate the key is 1 s. The keys generated have a uniqueness and reliability of 49.49% and 48.20%. The proposed protocol is independent of a communication, which makes it adaptable across multiple platforms.