Introduction: Cardiac autonomic dysfunction is a cardiovascular risk factor associated with various health conditions, mainly in overweight and obese individuals. In this regard, heart rate variability (HRV) is one of the tools that allow the evaluation of the activity of the autonomic nervous system (ANS), facilitating the physiological characterization and diagnosis of any individual. Objective: To determine the effect of physical exercise on heart rate variability (HRV) in adults (>18 years old) with overweight or obesity. Materials and methods: Systematic review. Cochrane, Medline, Embase, Lilacs, and PEDro databases were systematically searched using the following search strategy: types of study: randomized controlled trials (RCTs) assessing the effect of exercise-based interventions on HRV parameters in adults with overweight or obesity; publication period: January 2015 to June 2021; Language: English; search terms: MeSH terms combined with Boolean operators “AND” and “OR”. The review protocol was registered in PROSPERO (code: CRD42021224027). The risk of bias was assessed using the Cochrane risk of bias assessment tool. A random-effects meta-analysis was performed to estimate the pooled effect for each outcome variable (HRV parameter) when the pooling of data was possible. Subgroup analyses were also performed to make comparisons between the different interventions. A significance level of p<0.05 was considered. Results: The initial searches yielded 2650 studies; of these,only 10 RCTs met the inclusion criteria. There were no statistically significant differences between the intervention and control groups in terms of changes in the HRV parameters: standard deviation of normal-to-normal R-R (NNN) intervals (SDNN): weighted mean difference (WMD)=1.30, 95%CI:-5.93-8.53, p-value=0.72); root mean square of successive RR intervals differences (RMSSD): (WMD=0.79, 95%CI:-0.29-1.87, p-value=0.15); high frequency (HF): (WMD=6.67, 95%CI:1.71-11.63, p-value=0.008), and low frequency (LF): (WMD=-0.32, 95%CI:-0.73-0.10, p-value=0.13). Conclusions: Physical exercise did not affect any of the HRV parameters studied in adults with overweight or obesity.