Abstract We developed an FPGA-based high-speed readout system for a complementary metal-oxide-semiconductor (CMOS) image sensor to observe soft X-ray transients in future satellite missions, such as HiZ-GUNDAM. Our previous research revealed that the CMOS image sensor has low-energy X-ray detection capability (0.4–4 keV) and strong radiation tolerance, which satisfies the requirements of the HiZ-GUNDAM mission. However, CMOS sensors typically have small pixel sizes (e.g., ∼10 µm), resulting in large volumes of image data. GSENSE400BSI has 2048×2048 pixels, producing 6 Mbyte per frame. These large volumes of observed raw image data cannot be stored in a satellite bus system with a limited storage size. Therefore, only X-ray photon events must be extracted from the raw image data. Furthermore, the readout time of CMOS image sensors is approximately ten times faster than that of typical X-ray CCDs, requiring faster event extraction on a timescale of ∼0.1 s. To address these issues, we have developed an FPGA-based image signal processing system capable of high-speed X-ray event extraction onboard without storing raw image data. The developed compact system enabled mounting on a CubeSat mission, facilitating early in-orbit operation demonstration. Here, we present the design and results of the performance evaluation tests of the proposed FPGA-based readout system. Utilizing X-ray irradiation experiments, the results of the X-ray event extraction with the onboard and offline processing methods were consistent, validating the functionality of the proposed system.