Depression is a serious disorder disproportionately affecting people with chronic diseases, yet, to date is rarely recognized comorbidity in pediatric rheumatology clinical routine care. The aim of this study was to investigate the prevalence of depressive symptoms and depression in children with Juvenile idiopathic arthritis (JIA) and to identify associations to risk factors. Depressive symptoms were assessed using the Beck’s Depression Inventory (BDI)-Fast Screen Questionnaire validated for ages 13 and older and confirmed by the BDI or Hamilton Depression Scale. A cross-sectional analysis of 148 patients attending the rheumatology outpatient clinic of the Asklepios Children’s Hospital Sankt Augustin between January 2018 and May 2019 was performed. Possible associations between routinely assessed parameters of disease activity and treatment were analysed. 148 JIA patients (71.5% female), median age 14.7 years, were included. The prevalence for depressive symptoms was 13% and for depression 9.5%, of which 71.4% were newly identified with depression. Significant associations with depressive symptoms included rheumatoid factor negative polyarthritis, higher pain scores, functional limitations, higher disease activity, decreased general well-being, higher number of medications taken and not being in remission. In addition, poor treatment response (persistent pain despite therapy) and failure to achieve minimal activity/remission of disease despite intensified therapy with biologics correlated significantly with depressive symptoms. Depressive symptoms are an important comorbidity in JIA. Early recognition and treatment of psychological distress is essential to prevent deterioration in quality of life and long-term prognosis. Consequently, treat-to-target principles should include mental health as a therapeutic goal.