In this work, design and experimental validation of an Extended State Observer (ESO) based robust predictive controller for flexible joint system is presented. An output tracking predictive controller is designed for control of flexible joint system. However, the controller requires accurate mathe matical model as well as output derivatives to be available for its implementation. In this work, the issues are addressed by estimating the plant uncertainty and output derivatives by using an ESO. The ESO estimates the output derivatives and modeling uncertainty simultaneously and the estimates are used in the predictive controller designed for nominal system. Closed loop stability of the overall system is established. Numerical simulation results of the proposed approach as applied to the flexible joint system are presented and it is shown that the ESO based predictive controller offers improved performance. Finally, the efficacy of the proposed design is validated through experiments carried on Quanser's flexible joint module. The results show that the ESO based design offers superior performance in presence of significant plant uncertainty.