In this article, modeling and control of a rotating hub-beam system are studied. The system consists of a solid rotating cylinder and an attached flexible arm with a payload at the end. The rotation is supposed to be in the presence of gravity and the flexible arm is assumed to be a Euler-Bernoulli beam. To derive the equations of motion of the system, Lagrange’s method is applied. Moreover, Galerkin’s technique is employed to discretize the equations of motion. Furthermore, designing an appropriate two-time (slow and fast) scale controller in the presence of uncertainties is considered in order to track the desired hub angular position and suppress vibrations of the arm simultaneously. For the so-called slow subsystem, a novel controller design is proposed as two different cases, with and without the presence of uncertainties in system dynamics are considered; and accordingly, a control law for tracking the desired path is introduced based on the idea of using the cross-term constructed Lyapunov function. For the fast subsystem, a pole placement technique is used to suppress vibration of the beam. The simulation results indicate notable effectiveness of the proposed controller.