Rehabilitation Exoskeleton is becoming more and more important in physiotherapists’ routine work. To improve the treatment performance, such as reducing the recovery period and/or monitoring and reacting to unpredictable situations, the rehabilitation manipulators need to help the patients in various physical trainings. A special case of the active disturbance rejection control (ADRC) is applied to govern a proper realisation of basic limb rehabilitation trainings. The experimental study is performed on a model of a flexible joint manipulator, whose behaviour resembles a real exoskeleton rehabilitation device (a one-degree-of-freedom, rigid-link, flexible-joint manipulator). The fractional (FADRC) is an unconventional model-independent approach, acknowledged as an effective controller in the existence of total plant uncertainties, and these uncertainties are inclusive of the total disturbances and unknown dynamics of the plant. In this work, three FADRC schemes are used, the first one using a fractional state observer (FSO), or FADRC1, second one using a fractional proportional-derivative controller (FPD), or FADRC2, and the third one a Multi-loop fractional in PD-loop controller and the observer-loop (Feedforward and Feedback), or FADRC3. The simulated Exoskeleton system is subjected to a noise disturbance and the FADRC3 shows the effectiveness to compensate all these effects and satisfies the desired position when compared with FADRC1 and FADRC2. The design and simulation were carried out in MATLAB/Simulink.