We examined if manualized cognitive behavioral therapy (CBT) was more effective than Treatment As Usual (TAU) for clinically depressed adolescents within routine care. This multisite Randomized controlled trail included 88 clinically depressed adolescents (aged 12-21 years) randomly assigned to CBT or TAU. Multiple assessments (pre-, post treatment and six-month follow-up) were done using semi-structured interviews, questionnaires and ratings and multiple informants. The primary outcome was depressive or dysthymic disorder based on the KSADS. Completers, CBT (n = 19) and TAU (n = 26), showed a significant reduction of affective diagnoses at post treatment (76% versus 76%) and after six months (90% versus 79%). Intention-to-treat analyses on depressive symptoms showed that 41.6% within CBT and 31.8% within the TAU condition was below clinical cut-off at post treatment and after six-months, respectively 61.4% and 47.7%. No significant differences in self-reported depressive symptoms between CBT and TAU were found. No prediction or moderation effects were found for age, gender, child/parent educational level, suicidal criteria, comorbidity, and severity of depression. We conclude that CBT did not outperform TAU in clinical practice in the Netherlands. Both treatments were found to be suitable to treat clinically referred depressed adolescents. CBT needs further improvement to decrease symptom levels below the clinical cut-off at post treatment.