Background: Obesity is a major public health issue globally which is intrinsically linked to reduced heart rate variability (HRV). Physical inactivity and reduced resting HRV are linked to an increased risk of coronary heart disease, while athletes have a greater HRV. However, the exact correlation between physical activity and HRV remains uncertain. This systematic review aims to collect, report, and critically assess the current scientific literature about the association between physical activity and HRV in individuals with higher weight and obesity. Methods: A systematic search was carried out in electronic databases (Medline/PubMed, SCOPUS and CINAHL Plus) to retrieve studies that evaluated the relationship between physical activity and HRV in individuals with higher weight and obesity. Case-control, longitudinal/cohort, cross-sectional and observational studies were included. Using a critical narrative approach, information about the HRV, and physical activity was extracted and synthesized. The study was registered in PROSPERO: CRD42020208018 on October 9 2020. Results: After removing duplicates, 980 title/abstract records were checked for eligibility, and 12 papers were finally included in the narrative synthesis. The included studies contained physical activity as well as HRV in adults with higher weight or obesity with or without comorbidities. A negative relationship between moderate to vigorous physical activity and HRV indices had been found in two studies. There was also a negative relationship between sedentary time and HF (p = 0.049) and LF/HF (p = 0.036), as well as a positive relationship between sedentary time and LF (p = 0.014). Also dose-response association was found between vigorous exercise and higher SDNN, LF power, and HF power in one of the studies. Conclusions: This systematic review revealed a wide range of responses to physical activity and HRV; however, the current evidence uses a variety of approaches to objectively assess physical activity and measure HRV with different equipment.