With the automotive industry moving towards fully autonomous systems, the secure onboard communication is a necessity. Traditional cryptographic algorithms, such as RSA and ECC are threatened by the future threat quantum computers will pose and cannot be used any more. To overcome this, the study presents the Quantum Resilient Secure Onboard Communication (QRSecOC) protocol, a new hybrid cryptographic framework that combines classical cryptographic algorithms and Post Quantum Cryptography (PQC) in order to secure automotive networks. QRSecOC protocol protects data transmission over the Controller Area Network (CAN) between ECUs within a vehicle making sure its integrity, confidentiality and authentication. The protocol's key desirable features include adaptive encryption that enables it to dynamically change security levels according to real time threat assessments, as well as optimization mechanisms to reduce latency and reduce the needed computational overhead. Simulation results show that the use of the QRSecOC protocol results in a reduction of encryption latency by 47.3% with respect to RSA, while energy efficiency is improved by 23.2%. On top of that, the protocol achieves a twice higher security level with respect to traditional cryptographic techniques, providing robust protection from quantum enhanced attacks. Despite a 9.8% increase in computational overhead caused by embedding PQC, the system stays well under the computational power of automotive ECUs. Other than being a highly efficient solution for real time automotive applications, the protocol benefits from an increased throughput of 88.9%. Quantum threat is emerging and it is proposed that integrating the QRSecOC protocol provides a comprehensive solution that offers efficient secure communication for the future autonomous vehicles; while retaining backward compatibility with existing vehicular systems.