To date, there is considerable evidence of the effectiveness of acupuncture in fibromyalgia syndrome (FM). However, it is not known in which body areas acupuncture is more effective. The objective of this study was to assess the improvements of pain induced by acupuncture in single body areas in patients with FM. In this open-label pragmatic study, FM patients in a state of high disease severity were consecutively enrolled and treated with a course of 8 weekly sessions of manual acupuncture. Patients were assessed with the Self-Administered Pain Scale (SAPS) of the Fibromyalgia Assessment Status at baseline and at the end of eight acupuncture sessions. Acupuncture sessions were all conducted with the same acupuncture formula (LV3, SP6, ST36, LI4, CV6, CV12, Ex-HN-3, and GV20) in each session and in each patient. Ninety-six FM patients completed the course of treatment. All the 16 body areas assessed by SAPS showed improvement in pain. A statistically significant improvement was achieved in 12 of the 16 body areas investigated, with the best results in abdomen and forearms (p = 0.001), while the worst results were registered for neck (p = 0.058), chest (p = 0.059), left buttock (p = 0.065), and right thigh (p = 0.052). The treatment has also shown significant effectiveness in improving fatigue and sleep quality (p < 0.0001). Acupuncture has a beneficial effect on pain in all body areas in FM patients with high disease severity, with the greatest effects in the abdominal region and in the forearms, allowing a personalization of the treatment.