Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating multi-systemic disease characterized by a complex, incompletely understood etiology. To facilitate future clinical and translational research, a multicenter German ME/CFS registry was established to collect comprehensive, longitudinal, clinical, epidemiological, and laboratory data from adults, adolescents, and children in a web-based multilayer-secured database. Here, we present the research protocol and first results of a pilot cohort of 174 ME/CFS patients diagnosed at two specialized tertiary fatigue centers, including 130 (74.7%) adults (mean age 38.4; SD 12.6) and 43 (25.3%) pediatric patients (mean age 15.5; SD 4.2). A viral trigger was identified in 160/174 (92.0%) cases, with SARS-CoV-2 in almost half of them. Patients exhibited severe functional and social impairment, as reflected by a median Bell Score of 30.0 (IQR 30.0 to 40.0) and a poor health-related quality of life assessed with the Short form-36 health survey, resulting in a mean score of 40.4 (SD 20.6) for physical function and 59.1 (SD 18.8) for mental health. The MECFS-R provides important clinical information on ME/CFS to research and healthcare institutions and, together with a multicenter ME/CFS biobank, will pave the way for research projects addressing the pathogenesis, diagnostic markers, and treatment options. Trial registration: ClinicalTrials.govNCT05778006.