This paper presents the development of an Active Disturbance Rejection Controller (ADRC) to address the trajectory tracking problem of a 2DOF (Degrees of Freedom) Serial Flexible Robot. The proposed approach leverages differential flatness theory to determine the system’s flat output, simplifying the trajectory tracking problem into a linear state feedback control with disturbance rejection. A set of a Generalized Proportional Integral Observer (GPIO) and Luenberger observers is employed to estimate the derivatives of the flat output and both internal and external disturbances in real time. The control law is experimentally validated on a 2DOF Serial Flexible Robot prototype developed by Quanser. Quantitative results demonstrate that the ADRC achieves superior performance compared to a partial state feedback control scheme, with a Mean Squared Error (MSE) as low as 1.0651e−5rad2 for trajectory tracking. The ADRC effectively suppresses oscillations, minimizes high-frequency noise and reduces saturation effects, even under external disturbances. These findings underscore the robustness and efficiency of the proposed method for underactuated flexible systems.