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Objectives To determine the prevalence of depressive and anxiety symptoms among young people 7 years and 9 years after inclusion in the multicentre, prospective inception cohort (ICON) of newly diagnosed patients with juvenile idiopathic arthritis (JIA) in Germany, and to identify factors associated with mental health problems at study inclusion and in the course of the disease.Methods Patients and controls (healthy peers, eg, friends of the same age and sex) from the ICON cohort (both ≥13 years) were assessed for mental health using the Patient Health Questionnaire-9 and the Generalised Anxiety Disorder Scale-7 at 7-year and 9-year follow-ups. Demographic and clinical characteristics, treatments and health-related quality of life (HRQoL) (Pediatric Quality of Life Inventory (PedsQL)) were documented at baseline and follow-up visits. Cross-sectional (analysis of variance or χ² tests at 7-year/9-year follow-up) and longitudinal analyses (generalised linear mixed models for PedsQL in follow-up from baseline) were conducted, respectively.Results A total of 344 patients (age 18.7±3.5 years, disease duration 9.2±1.8 years, 42% polyarthritis) and 224 controls (age 18.2±3.6 years) were evaluated. Moderate to severe symptoms of depression and anxiety were present in 13% and 10% of patients, respectively, compared with 7% and 2% of controls. Patients with moderate to severe psychological distress did not exhibit significantly higher physician-reported disease activity at inclusion and follow-up but reported worse patient-reported outcomes. These patients already showed reduced emotional functioning 3 months after diagnosis (p<0.001) and reported lower physical and emotional functioning (p<0.001) after the first year of specialised care compared with those without relevant mental health problems at long-term follow-up.Conclusion Poor emotional functioning at the start of care for JIA may be an indicator of future mental health issues. Therefore, HRQoL should be routinely assessed at treatment initiation to identify at-risk patients early and provide targeted support.