This study is concerned with developing a robust tracking control system that merges the optimal control theory with fractional-order-based control and the heuristic optimization algorithms into a single framework for the non-minimum phase pitch angle dynamics of Boeing 747 aircraft. The main control objective is to deal with the non-minimum phase nature of the aircraft pitching-up action, which is used to increase the altitude. The fractional-order integral controller (FIC) is implemented in the control loop as a pre-compensator to compensate for the non-minimum phase effect. Then, the linear quadratic regulator (LQR) is introduced as an optimal feedback controller to this augmented model ensuring the minimum phase to create an efficient, robust, and stable closed-loop control system. The control problem is formulated in a single objective optimization framework and solved for an optimal feedback gain together with pre-compensator parameters according to an error index and heuristic optimization constraints. The fractional-order integral pre-compensator is replaced by a fractional-order derivative pre-compensator in the proposed structure for comparison in terms of handling the non-minimum phase limitations, the magnitude of gain, phase-margin, and time-response specifications. To further verify the effectiveness of the proposed approach, the LQR-FIC controller is compared with the pole placement controller as a full-state feedback controller that has been successfully applied to control aircraft dynamics in terms of time and frequency domains. The performance, robustness, and internal stability characteristics of the proposed control strategy are validated by simulation studies carried out for flight conditions of fault-free, 50%, and 80% losses of actuator effectiveness.