This paper presents a composite controller for tip position tracking of flexible link manipulators. The main control challenge for flexible link manipulators is the non-minimum phase characteristics of the system. In this regard, an inner/outer control structure is proposed. As opposed to previous research in this area, the desired reference trajectory is robustly modified in an online scheme to minimize the tip tracking error utilizing the outer controller. The outer trajectory modifier is a [Formula: see text] synthesis based controller which modifies the reference trajectory of the inner loop in the uncertain situations. The inner loop controller is based on the Lyapunov redesign feedback linearization (LRFL) approach which is applied to alleviate the degrading effects of uncertainties and non-linearities presents in the dynamics of the flexible-link manipulator. In the inner loop, a conventional redefined output namely ‘close to the tip’ is considered to avoid the difficulties associated with the non-minimum phase behaviour of the main output (the tip). Conventional control strategies based on this choice of outputs lead to undesirable oscillations in the tip position. However, these oscillations are considerably minimized by applying the proposed outer loop trajectory modifier. Experimental and Simulation results are presented to illustrate the significant improvements in tip tracking performance over the conventional methods.