Purpose: We investigated sex differences in heart rate variability (HRV; a non-invasive indicator of autonomic nervous system) and its frequency-specific responses to whole-body vibration (WBV) at three distinct frequencies among elderly subjects. Methods: Data from 11 males and 13 females were analyzed across four randomized sessions of exposure: WBV at 15, 20, or 25 Hz with a 4 mm peak-to-peak displacement, or control (0 Hz) condition comprising three bouts of 1-minute exposure with 1-minute between-bout rests. HRV measurements were taken before and during the exposure. Results: At baseline, low-frequency power/LF (ms^{2}) were significantly lower in females than males (P < 0.05). During exposure, LF (ms^{2}), high-frequency power (ms^{2}), standard deviation of normal-to-normal intervals, root mean square of successive differences between RR intervals, standard deviation of the Poincaré plot perpendicular to the line-of-identity, and standard deviation of the Poincaré plot along the line-of-identity significantly increased at 20 Hz for males and 25 Hz for females (P < 0.05 to 0.005) compared to respective baselines. Conclusions: Elderly females tend to exhibit reduced autonomic nervous system function compared to males. Furthermore, our results indicate that WBV at 20 Hz for males and 25 Hz for females may be considered beneficial for enhancing HRV in the elderly.