In this paper, a robust fuzzy-tuned PID controller is proposed for the trajectory tracking and vibration control of a flexible joint manipulator system (FJMS) with parametric uncertainties. Flexible joint manipulators are widely used in industry due to their flexibility, light in weight and fast response, low cost, and low energy consumption. The dynamic modeling via Euler-Lagrange equation for a single link flexible joint manipulator system (FJMS) is presented first. By analyzing the characteristics of the high order linear system, the Fuzzy-Tuned PID control strategy is utilized. The parameters of classical PID controller are updated by the intelligent method of fuzzy logic. With the adaptivity to the parametric uncertainties from the system stiffness and moment of inertia, the contrived approach provides more efficient results compared to existing techniques in terms of vibration suppressions, time response, and overshoot. Finally, the effectiveness of the controller is corroborated through multiple experiments on the QUANSER's flexible joint manipulator system (FJMS).