In this study, we consider the anti-windup design as one of the approaches for the boundary control problem of a flexible manipulator in the presence of system parametric uncertainties, external disturbances and bounded inputs. The dynamics of the system are represented by partial differential equations (PDEs). Using the singular perturbation approach, the PDE model is divided into two simpler subsystems. With the Lyapunov's direct method, an adaptive boundary control scheme is developed to regulate the angular position and suppress the elastic vibration simultaneously and the adaptive laws are designed to compensate for the system parametric uncertainties and the disturbances. The proposed control scheme allows the application of smooth hyperbolic functions, which satisfy physical conditions and input restrictions, be easily realised. Numerical simulations demonstrate the effectiveness of the proposed scheme.