The stripe non-uniformity of infrared focal plane array strongly impact the image quality, thus the application of infrared focal plane array is strongly restricted. A real-time FPGA-based system for correcting the stripe non-uniformity was proposed. The system was based on Midway Infrared Equalization method and it could execute the correction in a single frame. Simulation results have demonstrated its efficiency and effectiveness in correcting the stripe non-uniformity. System architecture was optimized for the algorithm so that the system had relatively low FPGA resources consumption and high speed. The system can be embedded into the infrared focal plane array imaging and processing system as an independent module to realize a real-time stripe non-uniformity correction. Due to the previous features, the system has great functionality and extensibility and has a broad prospect in practical application.