Background Cognitive behavioral therapy (CBT) is an effective intervention to treat depressive disorders in youth. However, 50% of adolescents still have depressive symptoms after treatment, and 57% drop out during treatment. Online CBT interventions have proven to be effective in reducing depressive symptoms and seem promising as a treatment for depressed adolescents. However, combining online programs with face-to-face sessions seems necessary to increase their effectiveness and monitor for suicide risk. Objective In this study, we examine the effectiveness and cost-effectiveness of a blended CBT treatment protocol, a mixture of online and face-to-face CBT, as a treatment for clinically depressed adolescents. Methods A pragmatic quasi-experimental controlled trial will be conducted to study the effectiveness of a blended CBT treatment protocol, in which blended CBT is compared with face-to-face CBT (n=44) and treatment as usual (n=44); the latter two were collected in a previous randomized controlled trial. The same inclusion and exclusion criteria will be used: adolescents aged between 12 and 21 years, with a clinical diagnosis of a depressive disorder, and referred to one of the participating mental health institutions. Assessments will be conducted at the same time points: before the start of the intervention, during the intervention (after 5 and 10 weeks), postintervention, and at 6- and 12-month follow-ups. Results The primary outcome is the presence of a depression diagnosis at 12-month follow-up. Several secondary outcomes will be measured, such as depressive symptoms, quality of life, and suicide risk. Costs and effects in both conditions will be compared to analyze cost-effectiveness. Further, moderating (age, gender, alcohol and drug use, parental depression, and other psychopathology) and mediating effects (negative automatic thoughts, cognitive emotion regulation, attributional style) will be analyzed. Also, treatment characteristics will be studied, such as characteristics of the therapists, treatment expectancy, and therapeutic alliance. Dropout rates and treatment characteristics will be measured to study the feasibility of blended CBT. Conclusions This study will examine the effectiveness and cost-effectiveness of a blended CBT program in which depressed adolescents are treated in mental health care. Results of blended CBT will be compared with face-to-face CBT and treatment as usual, and implications for implementation will be reviewed. Trial Registration Dutch Trial Register (NTR6759); http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=6759 International Registered Report Identifier (IRRID) DERR1-10.2196/13434 RR1-10.2196/12654