All things considered, most drones operate independently and frequently in remote or unreachable areas through networks. Recently, such networks have integrated into our daily lives, gathering new opportunities and facilities. However, new security challenges arise from these integrations. Researchers have developed various authentication protocols over the past ten years to overcome the arising challenges. Nonetheless, most of the protocols provided failed to resist physical assaults. To solve this problem and improve other security characteristics, this chapter suggests a semi-centralized authentication protocol based on PUF for Drone-to-Drone communication. In our protocol, the gateway only generates PUF challenges when direct authentication between drones is achieved using the Computational Diffie–Hellman problem. Our protocol presents a significant improvement in computation overhead, requiring only 7.5 ms. Likewise, it demands an acceptable communication overhead compared to related protocols.