Childhood obesity has been linked to physical and psychological comorbidities that can be carried into adulthood. A bidirectional link between body weight and the stress system appears to exist, as cortisol may affect the regulation of appetite, while adiposity can affect cortisol secretion. Among the biological tissues used to evaluate cortisol concentrations, scalp hair can provide retrospective measures. The aim of this systematic review was to investigate the difference in hair cortisol concentrations between obese and non-obese minors ≤ 19 years of age. Children and adolescents with genetic, somatic or psychiatric comorbidities were excluded. The work was conducted following the PRISMA guidelines, using prespecified search terms in the Pubmed database. The initial search yielded 56 studies, while the last step of the screening procedure concluded in 9 observational studies. Among them, the results could be characterized as inconclusive. Five of them demonstrated significantly higher hair cortisol concentrations in obese children and adolescents than normal weight subjects. On the contrary, the remaining four found no statistically significant differences in hair cortisol concentrations between obese and non-obese subjects. Different methodologies applied, and confounding factors could explain the inconsistency in the findings. Further research is needed to provide more solid results.