This study investigates the challenges associated with achieving synchronized arrivals in unmanned aerial vehicle (UAV) formations through an integrated approach to trajectory optimization and waypoint allocation. By implementing advanced optimization algorithms, including the Hungarian method, and utilizing Dubins paths for controlled trajectory adjustments, this methodology ensures that all UAVs reach their designated waypoints concurrently, complying with predefined speed and heading constraints. Simulations conducted within a digital twin environment validate the effectiveness of the approach, demonstrating significant reductions in total path length and formation time, thereby enhancing operational efficiency. We introduce innovative modifications to traditional trajectory planning by focusing on minimal adjustments to the initial turning radius, which maintains compliance with trajectory requirements while optimizing the formation’s dynamic responses. The proposed strategies enhance operational adaptability to various initial conditions and offer marked improvements over traditional methods in convergence speed and efficiency.