We investigated the extent to which obesity could identify autonomic dysfunction of heart control in a cross-sectional study with 65 women (aged 18-45 years), categorized as eutrophic, overweight or obese. We collected anthropometric measures and measures of heart rate variability (HRV) between March 2015 and March 2017. Low frequency in normalized units (LF (nu) ) over 46 was considered a marker of autonomic imbalance and high frequency in normalized units (HF (nu) ) below 38 a marker of depressed vagal modulation. Overweight (mean difference MΔHF (nu) = −13.11 [95% confidence interval (CI) of difference, −25.88, −0.34], Hedges's g = 0.65, common language effect size (CL) = 68.1%) and obese (MΔHF (nu) = −21.22 [95% CI, −31.89, −10.55], Hedges's g = 1.17, CL = 79.2%) women presented depressed vagal modulation compared to eutrophic women. Autonomic imbalance increased as body mass index increased (eutrophic-to-overweight MΔLF (nu) = 13.06 [95% CI, 1.65, 24.47], g = 0.65, CL = 67.9%, and overweight-to-obese MΔLF (nu) = 21.07 [95% CI, 10.32, 31.82], g = 1.15, CL 78.9%). The odds ratio for depressed HF (nu) among overweight women was 2.36 (95% CI 0.77, 7.29) and 2.18 among obese women (95% CI 0.79, 5.99), as well as 9.17 (95% CI 2.62, 32.04) and 17.39 for increased LF (nu) (95% CI 2.13, 141.76), respectively. The parasympathetic activity is diminished and autonomic imbalance of the cardiac control increased with increasing BMI categories.