BACKGROUND & AIMS: The effects of calorie restriction and physical activity on autonomic regulation and cardiac vagal control in overweight and obese individuals remain inconsistent. Thus, this systematic review aimed to evaluate the weight loss effects through lifestyle changes on heart rate variability (HRV) markers in overweight and obese subjects. METHODS: A systematic search for studies published up to November 2021 was conducted in MEDLINE, Embase, EBSCO host and VHL REGIONAL/LILACS. The main outcomes were changes in HRV indices from pre- and post-nutritional intervention and exercise in overweight and obese individuals. This review was registered in PROSPERO: CRD42021274467. RESULTS: The literature search retrieved 959 articles, of which 12 were included in this review. The intervention in nine studies was diet only, in two studies was diet and exercise, and in one study diet was compared to diet and exercise. The weight loss was greater than 10% in four studies and between 5 and 10% in three studies. Most of the studies revealed that weight loss through lifestyle changes seems to promote beneficial effects on HRV, restoring sympathovagal balance by increasing parasympathetic activity and reducing sympathetic activation. CONCLUSION: This systematic review exhibited the beneficial effects of weight loss through lifestyle changes on cardiac autonomic control in overweight and obese individuals. Future investigations need standardization of HRV indices for better interpretation of autonomic function in different clinical situations.