The non-minimum phase characteristic of a flexible manipulator makes tracking control of its tip difficult. The level of the tip tracking performance of a flexible manipulator is significantly affected by the characteristics of the tip reference trajectory as well as the characteristics of the flexible manipulator system. This paper addresses the question of how to best specify a reference trajectory for the tip of a flexible manipulator to follow in order to achieve the objectives of reducing : tip tracking error, residual tip vibration, and the required actuation effort at the manipulator joint. A novel method of tip-based learning controller for the flexible manipulator system is proposed in the paper, where a model of the flexible manipulator system with a command shaping filter is used to generate a smooth and realizable tip reference trajectory for a tip-based learning controller.