This paper presents the development, stability analysis and validation of an intelligent proportional integral (iPI) controller for the tip position control of a flexible-link manipulator. A stability analysis included in the paper shows that the iPI controller is equivalent to the proportional integral-squared controller. In order to verify the performance of the iPI controller, several experiments were conducted. In these experiments, step and square-wave inputs and two other trajectories were applied to the flexible-link manipulator. Also, the performance of the iPI controller was compared with those of classical PI and PID controllers. The results obtained from the comparison experiments showed that, the PI and PID controllers produced better performance in step and square-wave inputs, but the iPI controller yielded better trajectory tracking performance. All of the controllers were tested for disturbance and noise rejection capability. The iPI controller eliminated disturbance and noise better than the classical controllers. Considering all of the results, the iPI controller has great potential in trajectory tracking control of flexible-link manipulators.