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In this paper, a feedback linearization (FL)-based control law made implementable using an extended state observer (ESO) is proposed for the trajectory tracking control of a flexible-joint robotic system. The FL-based controller cannot be implemented unless the full transformed state vector is available. The design also requires exact knowledge of the system model making the controller performance sensitive to uncertainties. To address these issues, an ESO is designed, which estimates the state vector, as well as the uncertainties in an integrated manner. The FL controller uses the states estimated by ESO, and the effect of uncertainties is compensated by augmenting the FL controller with the ESO-estimated uncertainties. The closed-loop stability of the system under the proposed observer-controller structure is established. The effectiveness of the ESO in the estimation of the states and uncertainties and the effectiveness of the FL + ESO controller in tracking are demonstrated through simulations. Lastly, the efficacy of the proposed approach is validated through experimentation on Quanser's flexible-joint module.