Heart Rate Variability (HRV) represents cardiac autonomic behavior and have been related to menopausal symptoms, mainly vasomotor symptoms and their imbalance to cardiovascular risk. It is not clear in the literature which index represents this imbalance and what is their involvement with the menopausal state. The aim of this study was to evaluate HRV in menopausal transition and post-menopausal symptoms with different intensities. This cross-sectional study was conducted in Rio Branco, State of Acre, Brazil from October 2016 to July 2017. We used Kupperman-Blatt Menopausal Index (KMI) to measure menopausal symptoms intensity. HRV analysis was performed based on the guidelines of the European Society of Cardiology and the North American Society of Pacing and Electrophysiology. HRV is lower in the group with moderate/intense menopausal symptoms compared to mild symptoms. (RMSSD: p = 0.005, Cohen's d = 0.53, pNN50: p = 0.0004, Cohen's d = 0.68; HF: p = 0.024, Cohen's d = 0.44). There was association between HRV and KMI (RMSSD: r = -1.248, p = 0.004; and pNN50: r = -0.615, p: 0.029) in inverse relation to the intensity of vasomotor symptoms in women in TM. In conclusion, HRV was able to distinguish menopausal symptoms, indicating reduced vagal control in women with more intense symptoms.