A Base Station (BS) apparatus for estimating a velocity of a Mobile Station (MS) in a mobile communication system includes a channel estimator for performing channel estimation according to a velocity band, receiving a wireless channel signal from the MS, and performing channel estimation using channel estimation coefficients optimized for individual velocity bands; and a velocity estimator for dividing the velocity band into a plurality of sub-Doppler bands, detecting a sub-Doppler band including a frequency index having a maximum frequency response from among the divided sub-Doppler bands, and transmitting information of the detected sub-Doppler band to the channel estimator such that a channel estimation coefficient corresponding to the information is transmitted.