Objectives <p>Fibromyalgia imposes a considerable burden of disability worldwide, and its therapies include rehabilitation interventions. However, the overall brain modulatory effects of rehabilitation interventions and their effects on clinical improvements in patients with fibromyalgia remain unclear. This systematic review of magnetic resonance imaging studies synthesised evidence for the brain modulatory effects of rehabilitation in patients with fibromyalgia.</p> Methods <p>We searched PubMed, EMBASE, and Web of Science databases from inception to August 2023 for English articles on rehabilitation-induced brain function changes in patients with fibromyalgia. Methodological evaluation was performed using the Physiotherapy Evidence Database checklist.</p> Results <p>We included 17 studies with 416 participants reporting the brain modulatory effects of several rehabilitation methods (i.e. exercises, brain stimulation, cognitive behavioural therapy, nerve stimulation, and neurofeedback). These studies received fair to good scores on the Physiotherapy Evidence Database scale. Rehabilitation-induced changes in brain function were correlated with the presentation of fibromyalgia. From the included studies, baseline brain functions could successfully predict posttreatment changes in disease symptoms. However, limited evidence is available for the effects of rehabilitation on brain structure.</p> Conclusion <p>Rehabilitation was found to modulate brain functions to alleviate fibromyalgia symptoms and improve patients’ quality of life. This finding supports the hypothesis that brain modulation is one of the mechanisms underlying the rehabilitation-mediated mitigation of fibromyalgia. Our results suggest that brain function measured through functional magnetic resonance imaging can help predict the response of patients with fibromyalgia to rehabilitation programmes (PROSPERO registration number: CRD42023387612).</p>