In this paper, after complete modelling of a flexible satellite equipped with a control moment gyroscope (CMG) actuator, it is shown that a PD-like controller can globally asymptotically stabilize this satellite by using Lyapunov’s direct method. Despite the simplicity, simulations show that the controller can stabilize the flexible satellite in a three-axis manoeuvre even in the presence of external disturbances. Then, using a non-linear variable gains PD controller, which only uses angular velocity of the rigid body and the attitude parameters as the inputs, the performance of the control system is improved in some important aspects such as reducing maximum control torque, reducing maximum peak of deflection of the appendages and increasing robustness of the controller against the orbital disturbances. In addition, locally asymptotically stability of the non-linear variable gain PD controller is guaranteed using a novel Lyapunov candidate function. Considering the difficulty in measuring the appendages’ deflection and the primarily existence of parameter uncertainties, and as this controller is independent of changes in these parameters, such a control system is very useful and applicable. In order to validate the system’s mathematical model and the control system performance, an exact model of the satellite is constructed in the ADAMS/View software that is linked to the MATLAB software. The efficacy of the proposed approach is demonstrated by several numerical examples.