Background: The cardioprotective effect of physical exercise has been demonstrated in several studies. However, no systematic or updated analysis has described the effects of physical exercise on cardiovascular autonomic modulation in postmenopausal women. Aim: to describe the effects of physical exercise on cardiovascular autonomic modulation in postmenopausal women. Methods: The Scopus, PubMed, and Embase databases were searched for randomized clinical trials published between January 2011 and December 2021, and regarding the effects of physical exercise on cardiovascular autonomic modulation in postmenopausal women. Two independent authors processed the citations. The methodological quality was evaluated using the PEDRo scale. Results: Of the 91 studies identified, only 8 met the inclusion criteria, of which 7 had fair or poor methodological quality. The analyzed studies investigated the effects of functional training, whole-body vibration, muscular resistance, stretching, and aerobic exercises performed at home or at the gym. The majority of these exercise modalities showed improvements in heart-rate variability (HRV) indices and in the low-frequency band of blood pressure variability. The meta-analysis shows that exercise increased the standard deviation of instantaneous beat-to-beat variability (SD1) (mean difference (MD) = 3.99; 95% confidence interval (CI) = 1.22 to 6.77, n = 46; I2: 0%) and the standard deviation of long-term variability (SD2) (MD = 11.37; 95% CI = 2.99 to 19.75; n = 46; I2: 0%). Conclusions: Aerobic exercise and some nonconventional training modalities may have beneficial effects on cardiovascular autonomic modulation in postmenopausal women. More high-quality studies are still needed to further confirm their efficacy and safety.