In this article, an observer‐based adaptive boundary iterative learning control law is developed for a class of two‐link rigid‐flexible manipulator with input backlash, the unknown external disturbance, and the endpoint constraint. To tackle the backlash nonlinearities and ensure the vibration suppression, the disturbance observers based upon the iterative learning conception are considered in the adaptive boundary control design. A barrier Lyapunov function is incorporated with boundary control law to restrict the endpoint state. Based on the defined barrier composite energy function, the tracking angle error convergence of the rigid part is guaranteed, and the vibrations of the flexible part are suppressed through the rigorous analysis. Finally, a numerical simulation is provided to illustrate the effectiveness of the proposed control.