The L-band Digital Aeronautical Communications System (LDACS) is a key advancement for next-generation aviation networks, enhancing Communication, Navigation, and Surveillance (CNS) capabilities. It operates with VHF Datalink mode 2 (VDLm2) and features a seamless handover mechanism to maintain uninterrupted communication between aircraft and ground stations (GSs), improving safety and efficiency in air traffic management (ATM). However, LDACS’ handover process encounters significant security risks due to inadequate authentication and key agreement between aircraft and ground station controllers (GSCs) during handovers. This vulnerability threatens communications’ confidentiality, integrity, and authenticity, posing risks to flight safety and sensitive data. Therefore, developing and implementing a robust security framework to protect aviation communications is essential. In response, we have proposed a security solution specifically designed to protect LDACS handovers. Our solution uses a mutual authentication and key agreement mechanism tailored for LDACS handovers, ensuring robust security for all types of handovers, including Intra GSC - Intra Aeronautical Telecommunication Network (ATN), Inter GSC - Intra ATN, and Inter GSC - Inter ATN. Our approach utilizes post-quantum cryptography to protect aviation communication systems against potential post-quantum threats, such as unauthorized access to flight data, interception of communication, and spoofing of aircraft identity. Furthermore, our proposed solution has undergone a thorough informal security analysis to ensure its effectiveness in addressing handover challenges and offering robust protection against various threats. It seamlessly integrates with the LDACS framework, delivering low Bit Error Rate (BER) and latency levels, making it a highly reliable approach in practice.