In this paper, a new stereo 3D moving-target tracking system using the MSE (mean square error) and BPEJTC (binary phase extraction joint transform correlator) algorithms is proposed. A moving target is extracted from the sequential input stereo image by applying a region-based MSE algorithm following which, the location coordinates of a moving target in each frame are obtained through correlation between the extracted target image and the input stereo image by using the BPEJTC algorithm. Through several experiments performed with 20 frames of the stereo image pair with $640{ imes}480$ pixels, we confirmed that the proposed system is capable of tracking a moving target at a relatively low error ratio of 1.29 % on average at real time.