Currently, space robots such as planetary robots and flexible-link manipulators (FLMs) are finding specific applications to reduce the cost of launching. However, the structural flexible nature of their arms and joints leads to errors in tip positioning owing to tip deflection. The internal model uncertainties and disturbance are the key challenges in the development of control strategies for tip-tracking of FLMs. To deal with these challenges, we design a tip-tracking controller for a two-link flexible manipulator (TLFM) by developing a sampled-data extended state observer (SD-ESO). It is designed to reconstruct uncertain parameters for accurate tip-tracking control of a TLFM. Finally, a backstepping (BS) controller is designed to attenuate the estimation error and other bounded disturbances. Convergence and stability of the proposed control system are investigated by using Lyapunov theory. The benefits (control performance and robustness) of the proposed SD-ESO-based BS controller are compared with other similar approaches by pursuing both simulation and experimental studies. It is observed from the results obtained that SD-ESO-based BS Controller effectively compensates the deviation in tip-tracking performance of TLFM due to non-minimum phase behavior and model uncertainties with an improved transient response.