Non-linearity and flexibility of a joint of SCARA Robot are more problematic in controller and challenging with Fuzzy Supervisory controller. In this research, the prototype flexible-joint robot was designed and tested.Dynamic model of the prototype was described by energy method; Lagrange equation was used to find the equation of motion. The experiment with a fuzzy controller was implemented with the prototype SCARA robot to find the tracking performance. The controller was comparing with the alternative PID controller. Fuzzy logic controller was significant reducing the residualvibration of links.