There has been considerable recent interest in the positioning of autonomous underwater vehicles (AUVs). Underwater acoustic positioning system (UAPS) are usually used to determine position and speed of the moving target in water environment. Generally, moving target speed is estimated by derivative of the target position with traditional method. However, this approach relies heavily on accuracy of positioning. Thus, this paper presents a novel method for estimation of target speed with the UAPS only, especially with long baseline (LBL) acoustic positioning system. The method is made by estimating the Doppler frequency shift of the received signals and solving the set of linear equations. It could depend less on positioning accuracy than the traditional method. What’s more, it works well even though the moving target is subjected to acceleration or jerk. With simulations by MATLAB, it is shown that the method achieves very good performance.