This study focuses on the innovative field of quantum synchronization for satellite-based navigation systems including Global Navigation Satellite Systems (GNSSs) and the Non-Terrestrial Network (NTN) component of future 6G networks integrating both communication and navigation services. By combining a four-qubit system with the theoretical approach of the Lindblad master equation, we transcend the inherent limits of standard synchronization techniques. This achievement represents a quantum leap in satellite-based positioning, highlighting the scalability and cost-effectiveness of our technique for smaller satellites. The study demonstrates the possibility of reducing synchronization errors to less than one meter, significantly improving the reliability and precision of satellite-based navigation systems. The results of this study may contribute to the future development of both user-centric localization systems (typically GNSS systems) and network-centric localization systems (typically through the NTN component of 6G networks), leading to better positioning performance, more flexible multi-functional systems with the potential to limit both cost and size of satellites.