Fibromyalgia syndrome (FMS) is a common chronic pain disorder and often occurs as a concomitant disease in rheumatological diseases. Managing FMS takes a complex approach and often involves various non-pharmacological therapies. Fasting interventions have not been in the focus of research until recently, but preliminary data have shown effects on short- and medium-term pain as well as on physical and psychosomatic outcomes in different chronic pain disorders. This single-arm observational study investigated the effects of prolonged fasting (3–12 days, <600 kcal/d) embedded in a multimodal treatment setting on inpatients with FMS. Patients who were treated at the Department of Internal Medicine and Nature-Based Therapies of the Immanuel Hospital Berlin, Germany, between 02/2018 and 12/2020 answered questionnaires at hospital admission (V0) and discharge (V1), and then again three (V2), six (V3), and 12 (V4) months later. Selected routine blood and anthropometric parameters were also assessed during the inpatient stay. A total of 176 patients with FMS were included in the study. The Fibromyalgia Impact Questionnaire (FIQ) total score dropped by 13.7 ± 13.9 (p < 0.001) by V1, suggesting an improvement in subjective disease impact. Pain (NRS: reduction by 1.1 ± 2.5 in V1, p < 0.001) and quality of life (WHO-5: +4.9 ± 12.3 in V1, p < 0.001) improved, with a sustainable effect across follow-up visits. In contrast, mindfulness (MAAS: +0.3 ± 0.7 in V1, p < 0.001), anxiety (HADS-A: reduction by 2.9 ± 3.5 in V1, p < 0.0001), and depression (HADS-D: reduction by 2.7 ± 3.0 in V1, p < 0.0001) improved during inpatient treatment, without longer-lasting effects thereafter. During the study period, no serious adverse events were reported. The results suggest that patients with FMS can profit from a prolonged therapeutic fasting intervention integrated into a complex multimodal inpatient treatment in terms of quality of life, pain, and disease-specific functional parameters. ClinicalTrials.gov Identifier: NCT03785197.