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Background: Heart rate variability (HRV) modulates both the sympathetic nervous system and the parasympathetic nervous system (PNS) of the autonomic nervous system. Mood disorder is one of the contributing factors to influence HRV. The warm-water footbath as a relaxing way is used to enhance the PNS. In this study, we intended to explore the association between HRV and a footbath in the mood disorder group. Methods: We recruited 14 young male study participants to receive a 30-minute warm-water footbath three times a week. Furthermore, we monitored the heart rates electrocardiographically before, during, and after the intervention. Results: This study showed that the footbath not only significantly enhanced standard deviation of NN (SDNN) intervals, high-frequency (HF) power, and low-frequency (LF) power during the first five minutes footbath (p < 0.01) but also increased all the parameters in five minutes after finishing the footbath. SDNN intervals, HF power, and LF power remained significantly upward in the next five minutes (p < 0.05). Conclusion: In line with previous studies, this study showed that a footbath elevated the PNS-related HRV parameters. We suggest that a warm-water footbath improves the PNS modulation possibly through baroreflex.