We propose and experimentally demonstrate a method for sampling frequency offset (SFO) estimation in optical communication systems based on periodically inserted identical binary prefix. Different from conventional cyclic prefix, binary prefix provides not only high tolerance to chromatic dispersion in dispersive fiber transmission, but also the ability to estimate SFO by simple receiver-side digital signal processing. Moreover, this binary prefix based scheme is generally applicable to any advanced modulation formats. A proof-of-concept experiment is conducted to quantify the accuracy and tolerance of the scheme in estimating SFO. It is found that over a wide SFO range up to 341 ppm, the estimation error is kept under 20 ppb and signals are recovered with the same quality as with zero-offset sampling. The experimental results also confirm that this method is tolerant to link signal-to-noise ratio loss and dispersion, showing no additional penalty after transmission over a 40-km standard single-mode fiber at 1550 nm.