This paper presents the design, stability analysis and experimental validation of a computationally non-intensive, model-free, intelligent proportional-integral (iPI) controller for flexible joint manipulators. In order to show the performance of the iPI controller, it is compared with classical proportional-integral and proportional-integral-derivative controllers. Based on this comparison, the iPI-controlled system achieved a better than 60% tracking accuracy for both kane trajectory and sine input tracking. The iPI controller also significantly reduced transient swings in the flexible joint of the manipulator, when tracking a train of pulses. Moreover, the iPI controlled system successfully eliminated both disturbances and noise effects from the dynamics of the manipulator.