It is possible to use a PD controller to get acceptable tracking to a joint angle trajectory of a single flexible link manipulator. However, it has a poor capability to damp out end effector vibrations at the end of the trajectory following phase. Another controller can be used at the end of this phase to damp out end effector vibrations excited during this phase. The paper suggests the start of application of the second controller at the midpoint of the trajectory phase, and not at its end. This idea under consideration is investigated by a SIMULINK model within MATLAB environment where better results concerning overshoot are obtained.