BACKGROUND: Prevalence rates of anxiety and depression in adolescence are rising markedly in early adolescence. It is important to quantify the non-fatal disease burden of anxiety and depression, such that early interventions can be well targeted, and resources can be allocated in a just and optimal way. This study aimed to estimate the non-fatal disease burden of anxiety and depression with and without suicidal ideation in girls and boys aged 13, 14, and 15 years. METHODS: Participants were 53,894 secondary school pupils who completed health questionnaires between September 2018 and July 2019. A design-based approach was used for complex survey data with post-stratification weights and taking clustering at school-level into account. At individual level, disability weights (DWs) were calculated for each disorder. At population level, DWs were multiplied by the point-prevalence per one thousand population of the respective disorders to compute years lived with disability (YLD). DWs and YLD of anxiety and depression were calculated with and without adjustment for comorbid eating disorders, substance use disorders and somatic illnesses. RESULTS: The unadjusted DW of depression with suicidal ideation (0.30) was greater than without suicidal ideation (0.26), and both were greater than the DW of anxiety (0.24). A similar ranking was obtained after adjusting for comorbidities. At population level, where the prevalence of the disorders come into play, the YLD disease burden was greatest for anxiety, followed by depression with suicidal ideation and depression without suicidal ideation with 17.40, 9.85, and 5.28 YLD per one thousand population, unadjusted for comorbidities. This pattern was the same after adjustment, but then the total YLD of depression with and without suicidal ideation was similar to the YLD of anxiety (12.47 and 12.46, respectively). Girls showed a significantly greater YLD burden of anxiety and depression than boys, but no differences were found between different age groups. CONCLUSIONS: From an individual clinical perspective, depression, especially when accompanied by suicidal ideation, was identified as a major health concern, especially in girls. From a public health perspective, both anxiety and depression, especially when accompanied by suicidal ideation, were identified as major drivers of disease burden, again most notably in girls.