A new controller for the end-effector trajectory tracking (EETT) of a class of flexible link manipulators which consists of a chain of rigid links with a flexible end-link (CRFE) is introduced. To design this new controller, a dynamic model of the CRFE is expressed in the singularly perturbed form; that is, decomposed into slow and fast subsystems. The states of the slow subsystem are the joints’ rotations and their time derivative, while the states of the fast subsystem are the flexible variables, which model the lateral deflection of the end-link, and their time derivative. For the slow subsystem, the new controller requires only ‘‘one’’ corrective torque in addition to the computed torque command of the rigid link counterpart of the CRFE for the reduction of the EETT error. This corrective torque is derived based on the concept of the integral manifold of the singularly perturbed differential equations. The need for only one corrective torque and its derivation are among the contributions of the new controller. To stabilize the fast subsystem, an observer-based controller is designed according to the gain-scheduling technique. Due to the application of the observer-based controller there is no need for the measurement of the time derivative of the flexible link’s lateral deflection, in which its measurement is difficult if not impossible in practice. This feature of the new controller is an advantage for it. To facilitate the derivation and implementation of this controller, several properties of the matrices in the dynamic model of the CRFE are introduced and used which are other contributions of this research. The effectiveness and feasibility of the new controller are shown by simulation and experimental studies.