Particle accelerators consist of an enormous number of components and many of them operate with pulse voltage or current. Such accelerator components require precise voltage or current to keep the beams very stable. For this reason, many pulse power supplies used for accelerators have own subsystems to improve their performances. One example is a power supply for the scanning magnets of a pencil beam proton therapy. They use not only high-voltage inverters for the high-speed ramping but also low-voltage inverters for the precise current control. However, the use of intelligent digital controllers possibly simplifies such precise power supplies. We propose a method for precise current control using a digital control system. Our previous work has successfully controlled the pulse current of power supplies for synchrotron main magnets. In the next step, we have modified our previous method for faster power supplies such as ones for scanning magnets. In addition, we developed a control board using a high-performance FPGA so that our method can be implemented in the board. In this paper, we describe the details of our proposed method, and the experiments using a small-scale power supply and the developed control board.