In fiber-optic Brillouin optical time-domain reflectometer (BOTDR) system, the estimation of the center frequency of Brillouin scattering spectrum in fiber is the key and the most time-consuming part of the measurement, which makes BOTDR system difficult to achieve fast response. In this paper, estimation of signal parameters via rotational invariance technique (ESPRIT) algorithm is proposed to estimate the center frequency of Brillouin scattering spectrum in BOTDR system. Due to fairly low requirement on data length, ESPRIT algorithm can obtain good frequency estimation over short data length, and makes it possible to increase measurement speed at high spatial resolution and measurement performance.