This paper proposes a prefilter type velocity compensating control system using modified chaotic neural networks for the trajectory control of robotic manipulator. Since the structure of modified chaotic neural networks(MCNN) and neurons have highly nonlinear dynamic characteristics, MCNN can show the robust characteristics for controlling highly nonlinear dynamics like robotic manipulators. For its application, the trajectory controller of the three-axis robot manipulator is designed by MCNN. The MCNN controller acts as the compensator of the PD controller. Simulation results show that learning error decrease drastically via on-line learning and the performance is excellent. The MCNN controller showed much better control performance and shorter calculation time compared to the RNN controller, Another advantage of the proposed controller could by attached to conventional robot controller without hardware changes.