This paper presents a novel artificial intelligence-based autopilot control system designed for the Cessna Citation X (CCX) aircraft longitudinal motion during cruise. In this control methodology, the unknown aircraft dynamics in the state-space representations of each vertical speed (VS) mode and altitude hold (AH) mode were approximated by two multiplayer fuzzy recurrent neural networks (MFRNNs) trained online using a novel approach based on particle swarm optimisation and backpropagation algorithms. These MFRNNs were used with two sliding mode controllers to guarantee the robustness of both VS and AH modes. In addition, a novel fuzzy logic-based transition algorithm was proposed to efficiently switch the controller between these autopilot modes. The performance of the controllers was evaluated with a nonlinear simulation platform developed for the CCX based on data from a Level D research aircraft flight simulator certified by the FAA. The system stability and robustness were proved by the Lyapunov theorem. The simulation, tested under 925 flight conditions, demonstrated the controllers exceptional tracking capability in a variety of uncertainties, including turbulent and non-turbulent flight scenarios. In addition, the design ensured that the smoothness of the control input signals was maintained in order to preserve the mechanical integrity of the elevator actuation system.