In this paper, nonlinear dynamical equations of the flexible manipulator with a lumped payload at the free end are derived from Hamilton's principle. The obtained model consists of both distributed parameters and lumped parameters, namely, partial differential equations (PDEs) governing the flexible motion of links and boundary conditions in the form of ordinary differential equations (ODEs). Considering the great nonlinear approximation ability of the radial basis function (RBF) neural network, we propose a combined control algorithm that includes two parts: one is a boundary controller to track the desired joint positions and suppress the vibration of flexible links; another is a RBF neural network designed to compensate for the parametric uncertainties. The iteration criterion of the RBF neural network weight matrix is derived from the extended Lyapunov function. Stabilization analysis is further carried out theoretically via LaSalle’s invariance principle. Finally, the results of the numerical simulation verify that the proposed control law can realize the asymptotic convergence of tracking error and suppression of the elastic vibration as well.