The prevalence of obesity continues to grow, resulting in metabolic syndrome and increasing economic burden for health systems. The objectives were to measure the ability of the NIM-MetS test, previously used in the adults, for the early and sustainable detection of the Metabolic Syndrome (MetS) in children and adolescents. Moreover, to determine the economic burden of the children with MetS. Furthermore, finally, to use and implement the NIM-MetS test, via a self-created online software, as a new method to determine the risk of MetS in children. The method used was an observational study using different instruments (NIM-MetS test, International Diabetes Federation (IDF), or Cook) and measures (body mass index). Additionally, the economic burden was estimated via a research strategy in different databases, e.g., PubMed, to identify previous papers. The results (N = 265 children, age from 10–12) showed that 23.1% had obesity and 7.2% hypertension. The prevalence of MetS using the NIM-Mets was 5.7, and the cost of these children was approximate 618,253,99 euros. Finally, a model was obtained and later implemented in a web platform via simulation. The NIM-MetS obtained is a non-invasive method for the diagnosis of risk of MetS in children.