Childhood and adolescence are pivotal periods for mental health. The hypothalamic-pituitary-adrenal axis is the primary stress system and its chronic activation is measurable via hair cortisol concentration (HCC), indicating long-term stress exposure. While HCC is linked to adult mental health, this relationship remains unclear among youth. Although a bidirectional relationship is possible, the impact of mental health problems on HCC in youths has been comparatively underexplored. This study aimed to assess the association between symptoms of mental health problems in childhood and adolescence and HCC levels at age 15 in a Brazilian population-based cohort. We analyzed data from the 2004 Pelotas Birth Cohort, which includes 4,231 children followed from birth. At ages 6, 11 and 15 years, mental health symptoms were assessed using the Strengths and Difficulties Questionnaire (SDQ). At age 15, HCC was measured from 3 cm hair samples, quantified through the enzyme-linked immunosorbent assay. To evaluate the cumulative impact of mental health symptoms from childhood to adolescence, group-based trajectory analysis was conducted. Subsequently, linear regression models were used to estimate associations between mental health scores and HCC, with adjustment for relevant covariates. Regression coefficients were exponentiated to improve interpretability. SDQ total difficulties (β = 1.004 [1.000
1.008]) and conduct problems (β = 1.017 [1.004
1.030]) at age 6 were associated with HCC at age 15 in adjusted models. Hyperactivity/inattention symptoms at ages 6 (β = 1.009 [1.001
1.018]) and 11 (β = 1.013 [1.004
1.022]) were associated with HCC in adjusted models. At age 15, hyperactivity/inattention symptoms and HCC was associated with HCC in the partially adjusted model (β = 1.009 [1.000
1.017]). Trajectories of chronic conduct problems and hyperactivity between ages 6 and 15 were also associated with elevated HCC, although for hyperactivity/inattention symptoms the association was not significant. These associations emphasize the links between mental health and chronic stress over time, especially between both conduct problems and hyperactivity/inattention symptoms in relation to higher concentrations of HCC.