ObjectiveChildren with intellectual disability (ID) usually exhibit neuroendocrine functioning impairment, such as alterations in the hypothalamic–pituitary–adrenal (HPA) neuroendocrine axis, which can result in glucocorticoid cortisol release alterations. Indeed, many studies showed a positive association between ID and cortisol concentration. However, evidence is lacking on the relationship between child neurodevelopment and cortisol levels during adolescence in population‐based studies. We aimed to test the association between ID and hair cortisol concentration (HCC) during adolescence in a prospective population‐based cohort.MethodsData from 1770 individuals in the 2004 Pelotas Birth Cohort were used. ID was diagnosed at age 6 through clinical examination. Hair cortisol was measured at age 15. Association was assessed using linear regression models adjusted for sex, socio‐economic factors, hair‐related variables and corticosteroid use.ResultsHigher HCC were observed in individuals with ID (β: 1.120; 95% CI: 1.012, 1.241) in the analysis adjusted for sex, hair‐related variables and corticosteroid use. Compared to the other aetiological groups, this was more evident in idiopathic ID. But this did not remain significant when demographics/socio‐economic variables were controlled for.ConclusionChildren with ID, particularly those with idiopathic ID, might exhibit dysfunction in the HPA axis or experience heightened stress levels during adolescence.