This study aims to synthesize and implement a robust fractional order PD (RFOPD) controller to increase the speed at which defects in automated touch panel inspection systems (ATPISs) are detected. A three-dimensional orthogonal stage (TDOS) driven by BLDC servo motors moves the inspection pen (IP) vertically and horizontally. The dynamic equation relating the BLDC servo motor input to the tip motion is established. A touch position identification (TPI) system is used to locate the touch point rapidly. An RFOPD controller is used to actuate the BLDC servo motors and move the TDOS rapidly and accurately in three dimensions. This method displaces the IP to any specified position and shows user-defined inspection trajectories on the touch screens. The gain-phase margin tester (GPMT) and stability equation methods are exploited to schedule the RFOPD controller gain settings and to maintain the specific safety margins for the controlled system. The simulation studies show that the proposed RFOPD controller exhibits better tracking and disturbance rejection responses than a conventional PID controller. The robustness of the RFOPD-controlled ATPIS, considering unmodeled uncertainties and friction-induced disturbances, is verified through simulation and experimental studies. Several user-defined inspection patterns are used to verify performance, and the experimental results show that the proposed RFOPD controller is effective.