A bird and bat monitoring system has been developed that uses marine radar, IR camera and acoustic recorders for wind farm applications. IR video recording is used to monitor birds and bats activity which will be useful for wildlife biologists in developing mitigation techniques to minimize impact of wind turbines on birds and bats. In order to process nocturnal migration data that is recorded from one hour after sun set to one hour before the sun rise requires high speed computations. IR video processing is computationally intensive. A parallel processing approach and use of GPU is proposed to process IR video data that will meet real time requirements. This paper examines the parallel implementation of the IR video processing on GPU.We achieved the real time requirements and the necessary performance for analyzing IR with size 704×480.