Recently, robots with rotary flexible joints have become widespread and important for many tasks that require flexibility, like refueling, inspections, and maintenance. However, controlling these types of joints is difficult because they are nonlinear, coupled, and under-actuated systems. The goal of this research is to achieve accurate trajectory tracking while minimizing vibrations in the joint. Therefore, the prescribed performance function (PPF) was combined with the Fractional-Order Proportional Integral Derivative (FOPID). By doing so, the proposed controller benefits from the enhanced transient phase performance of PPF as well as the simple structure, easy tuning, and enhanced performance of the FOPID. This paper outlines the design of a FOPID controller with a prescribed performance function for controlling a rotary flexible joint robot (RFJ). First, the FOPID is designed and tuned to get the best performance, and then a PPF is designed to improve the tracking performance of the FOPID during the transient phase and minimize the deflection angle. This is proved after comparing the performance of the proposed control strategy and the integer-order PID through the experiment.