<p>In this paper, a novel barrier function-based adaptive controller is proposed for an <i>n</i>-link flexible-joint (FJ) robotic system to accomplish the task of accurate trajectory tracking control in the presence of system model uncertainties, unknown external disturbances, and nonsmooth nonlinear inputs. Firstly, the traditional <i>n</i>-link robot system expressed by the Lagrangian dynamic function is remodeled as a fourth-order fully-actuated system by introducing the fully-actuated system theory. It results that the problems of complex controller design and computational explosion triggered by backstepping control method are solved successfully. Furthermore, under relaxed assumptions on system uncertainties, i.e., the upper boundary of the lumped system uncertainties is unknown, a barrier function-based adaptive sliding mode controller is designed, then the trajectory tracking errors of the system are ensured to converge into a neighborhood of zero in the presence of nonsmooth nonlinear control inputs. Particularly, the convergence errors independent of the upper boundary of system uncertainties can be determined in advance based on practical engineering application. Meanwhile, the closed-loop stability of the FJ robot system under the proposed adaptive controller is rigorously proved based on the Lyapunov stability theorem. Finally, the superior performance of the proposed control approach is demonstrated by the simulation results of a two-link FJ robot system and a comparison study.</p>