Median filter is usefiil in image and video processing. It can be used for filtering noises, for estimating background images, and so on. However, median filter is time-consuming. This paper presents a new method for realizing the median filter in GPU (Graphics Processing Unit) for background estimation problem. The proposed method can perform the filtering in just several milliseconds for each frame in high resolution videos. The experimental results show that the proposed method is even faster than the fastest GPU-based algorithms deployed in OpenCV for background estimation problem.