This paper introduces an FPGA based implementation for processing 2D images of laser Doppler blood flow. The method presented uses a high speed FPGA prototyping platform to achieve a basic frame rate of flow images at 1 frame/second for 256 x 256 pixels with 1024 FFTpoints, which is significantly higher than other systems reported to date. The frame rate can be further increased, without changing the design, if higher clock or multiple processing units are used. The processing system utilises a concurrent and pipeline processing scheme to obtain high-speed performance. Mixed fixed-floating point calculations are utilized to achieve high accuracy but low resource usage. Simulation and test results are illustrated demonstrating successful performance of the system. The relative error obtained using the processing unit is below 0.1% when compared with signals processed off-line on a PC.