Drones also called Unmanned Aerial Vehicles (UAVs) have become more prominent in several applications such as package delivery, real-time object detection, tracking, traffic monitoring, security surveillance systems, and many others. As a key member of IoT, the group of Radio Frequency IDentification (RFID) technologies is referred to as Automatic Identification and Data Capturing (AIDC). In particular, RFID technology is becoming a contactless and wireless technique used to automatically identify and track the tagged objects via radio frequency signals. It also has drawn a lot of attention among researchers, scientists, industries, and practitioners due to its broad range of real-world applications in various fields. However, RFID systems face two key concerns related to security and privacy, where an adversary performs eavesdropping, tampering, modification, and even interception of the secret information of the RFID tags, which may cause forgery and privacy problems. In contrast to security and privacy, RFID tags have very limited computational power capability. To deal with these issues, this paper puts forward an RFID-based Lightweight and Provably Secure Authentication Protocol (LPSAP) for Unmanned Aerial Vehicle Systems. The proposed protocol uses secure Physically Unclonable Functions (PUFs), Elliptic-Curve Cryptography (ECC), secure one-way hash, bitwise XOR, and concatenation operations. We use Ouafi and Phan’s formal security model for analyzing security and privacy features such as traceability and mutual authentication. The rigorous informal analysis is carried out which ensures that our proposed protocol achieves various security and privacy features as well as resists various known security attacks. The performance analysis demonstrates that our proposed protocol outperforms other existing protocols. In addition, Scyther and Automated Validation of Internet Security Protocols and Applications (AVISPA) tool simulation results demonstrates that there is no security attack possible within bounds. Therefore, our proposed LPSAP protocol achieves an acceptable high level of security with the least computational, communication, and storage costs on passive RFID tags.