Three weeks of exercise therapy altered brain functional connectivity in fibromyalgia inpatients

•Patients with fibromyalgia underwent a three-week exercise therapy on inpatient basis.•The three-week exercise therapy improved symptoms of fibromyalgia and patients motor ability.•Alterations of functional connectivity in sensorimotor cortices were related to improved symptoms of fibromyalgia.•Alterations of functional connectivity in the mesocortico-limbic system were related to improved motor ability of patients with fibromyalgia.•Alterations of functional connectivity by exercise therapy can be involved in the improvement of symptoms of fibromyalgia and patients’ motor ability.