Real control systems require robust control performance to deal with unpredictable and altering operating conditions of real-world systems. Improvement of disturbance rejection control performance should be considered as one of the essential control objectives in practical control system design tasks. This study presents a multi-loop Model Reference Adaptive Control (MRAC) scheme that leverages a nonlinear autoregressive neural network with external inputs (NARX) model in as the reference model. Authors observed that the performance of multi-loop MRAC-fractional-order proportional integral derivative (FOPID) control with MIT rule largely depends on the capability of the reference model to represent leading closed-loop dynamics of the experimental ML system. As such, the NARX model is used to represent disturbance-free dynamical behavior of PID control loop. It is remarkable that the obtained reference model is independent of the tuning of other control loops in the control system. The multi-loop MRAC-FOPID control structure detects impacts of disturbance incidents on control performance of the closed-loop FOPID control system and adapts the response of the FOPID control system to reduce the negative effects of the additive input disturbance. This multi-loop control structure deploys two specialized control loops: an inner loop, which is the closed-loop FOPID control system for stability and set-point control, and an outer loop, which involves a NARX reference model and an MIT rule to increase the adaptation ability of the system. Thus, the two-loop MRAC structure allows improvement of disturbance rejection performance without deteriorating precise set-point control and stability characteristics of the FOPID control loop. This is an important benefit of this control structure. To demonstrate disturbance rejection performance improvements of the proposed multi-loop MRAC-FOPID control with NARX model, an experimental study is conducted for disturbance rejection control of magnetic levitation test setup in the laboratory. Simulation and experimental results indicate an improvement of disturbance rejection performance.