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Downgrade alterations in the growth hormone (GH) might be involved in the development of some of the fibromyalgia syndrome (FMS) symptoms. Our aim was to assess the effects of an aerobic exercise programme on the GH levels in patients with FMS. A randomised controlled trial was developed. Sixty-four Spanish women with FMS were randomly assigned to the experimental arm (n = 33) and treated with a 16-week group physical exercise programme based on low impact aerobic dance (three weekly sessions, one-hour each), or to the treatment-as-usual (TAU) control arm (n = 31). The primary outcome was the GH response to acute exercise. Secondary outcomes were GH basal, sensitivity to pain, body composition, aerobic capacity, and quality of life. The ANCOVA results showed a moderate effect of treatment improving the GH response to acute exercise. Other effects were substantial for aerobic capacity, quality of life, and body composition. Pre-intervention GH response to acute exercise was related to improvements in aerobic capacity and quality of life. An aerobic exercise programme may improve the response of the GH, aerobic capacity, body composition, and quality of life in women with FMS. The normalization of neuro-hormonal patterns involving the GH might be key for improving some FMS symptoms.