This paper presents a simple and effective adaptive PDPID with ILC control scheme. The adaptive control scheme is for tuning PD control gains for two-link flexible manipulator and the ILC is to improve the overall system performance. The manipulator is modelled using Lagrange and assume mode method. The adaptive control scheme continuously tunes PD controller gains depending on the error value without switching. The proposed control law is tested in Matlab/Simulink simulation environment and its performance is compared with PDPID, PDPIDILC and adaptive PDPID controllers. The effect of constant disturbance, sine wave disturbance and white noise disturbances on the proposed controller is extensively studied. The results show the effectiveness and robustness of the proposed adaptive PDPID controller with iterative learning.