In this paper, a novel neural network-based robust iterative learning fault estimation scheme is proposed to address the problem of fault modeling and estimation in nonlinear manipulator systems with disturbances and parameter uncertainties. The aim is to enhance the rapidity, efficiency, and accuracy of fault estimation. Firstly, the modeling for flexible manipulator control system is constructed as a preparation of iterative learning fault estimation observer design. Then, the neural network model is constructed to optimize the gain parameters of iterative learning fault estimator to approximate nonlinear uncertainties. Additionally, a H∞ robust technique is used to suppress fault variation rate and disturbances, which enhances the speed of estimation and reduces the impact of disturbances. So that the estimated fault can rapidly and accurately track the actual fault over the whole time interval and iterations. Finally, numerical simulations are conducted to demonstrate the effectiveness of the proposed neural network-based robust iterative learning scheme.