Background <p>Chronic musculoskeletal pain (CMP) is a prevalent condition associated with significant disability. Emerging evidence suggests that autonomic dysfunction, reflected by heart rate variability (HRV), may play a role in the pathophysiology of CMP and could be responsive to exercise interventions. This systematic review aims to evaluate the effects of exercise on HRV in persons with CMP.</p> Methods <p>A comprehensive search was performed in PubMed, Web of Science, and Cochrane databases from database inception until June 15, 2024. Eligible studies included those examining exercise interventions of ≥ four weeks in adults aged 18 to 65 with CMP, where HRV was assessed both before and after the intervention. Non-experimental study designs and studies focusing exclusively on acute exercise effects were excluded. Two independent reviewers performed data extraction and assessed the risk of bias using the Cochrane RoB-2 and ROBINS-I tools. The CERT was used for reporting, and effect sizes for exercise interventions were calculated. Certainty of evidence was assessed using the GRADE framework.</p> Results <p>Five randomized and five non-randomized controlled trials were included, involving 277 persons with CMP. There was considerable variability in HRV measurement protocols. The exercise interventions, which included resistance, aerobic, and multi-component training, lasted four to 24 weeks. Significant within-group improvements were found in several HRV measures, especially in linear analyses linked to vagal modulation at rest.</p> Conclusions <p>While evidence suggests the positive influence of exercise on autonomic function in CMP, as indicated by HRV changes, the limited number of high-quality studies warrants cautious interpretation. To better understand the impact of different exercise modalities on HRV and address existing data gaps, future research should implement strict protocols for HRV measurements and consistently adhere to established reporting criteria for exercise interventions.</p>