In this paper, a high-performance control system based on field programmable gate arrays (FPGAs) for a 6-UPS medical parallel robot is present. The control system utilizes the hardware and software reconfigurable feature of the advanced FPGA device to achieve our goal. Firstly, the parallel robot and its control system components and functions are introduced. Secondly, the control system general description including its hardware is given. Thirdly, NIOS II soft core processor module, HALL module, PWM signal module, DC motor drive module, encoder signal processing module, and the soft-core software are designed in detail. All the modules can be duplicated and reconfigured to control as many motors as needed. Finally, to estimate the control system, a driving test based on RS232 is carried out. Satisfactory test results demonstrate that the FPGA-based control system is a flexible, high-performance solution to the motion control of our 6-UPS medical parallel robot.