Abstract Background Depressive disorders occur in 2 to 5% of the adolescents and are associated with a high burden of disease, a high risk of recurrence and a heightened risk for development of other problems, like suicide attempts. The effectiveness of cognitive behaviour therapy (CBT), cost-effectiveness of this treatment and the costs of illness of clinical depression in adolescents are still unclear. Although several Randomized Controlled Trials (RCT) have been conducted to establish the efficacy of CBT, the effectiveness has not been established yet. Aim of this study is to conduct a RCT to test the effectiveness of CBT and to establish the cost-effectiveness of CBT under rigorous conditions within routine care provided by professionals already working in mental health institutions. Method/Design CBT is investigated with a multi-site, RCT using block randomisation. The targeted population is 140 clinically referred depressed adolescents aged 12 to 21 years old. Adolescents are randomly assigned to the experimental ( N  = 70, CBT) or control condition ( N  = 70, TAU). Four assessments (pre, post, follow up at 6 and 12 months) and two mediator assessments during treatment are conducted. Primary outcome measure is depression diagnosis based on a semi-structured interview namely the K-SADS-PL. Secondary outcome measures include depressive symptoms, severity and improvement of the depression, global functioning, quality of life, suicide risk, comorbidity, alcohol and drug use, parental depression and psychopathology, parenting and conflicts. Costs and treatment characteristics will also be assessed. Furthermore, moderator and mediator analyses will be conducted. Discussion This trial will be the first to compare CBT with TAU under rigorous conditions within routine care and with a complex sample. Furthermore, cost-effectiveness of treatment and cost-of-illness of clinical depression are established which will provide new insights on depression as a disorder and its treatment. Trial registration Dutch Trial register number NTR2676 . The study was financially supported by a grant from ZonMw, the Netherlands organization for health research and development, grant number 157004005.