BACKGROUND: Behavioral health services for children and adolescents in the U.S. are lacking in accessibility, availability and quality. Evidence-based interventions for emotional and behavioral disorders can improve quality, yet few studies have systematically examined their implementation in routine care settings. METHODS: Using quantitative and qualitative data, we evaluated a multi-faceted implementation strategy to implement cognitive-behavioral therapy (CBT) for depressed adolescents into two publicly-funded mental healthcare centers. Extent of implementation during the study's duration and variables influencing implementation were explored. RESULTS: Of the 35 clinicians eligible to participate, 25 (71%) were randomized into intervention (n = 11) or usual care (n = 14). Nine intervention clinicians completed the CBT training. Sixteen adolescents were enrolled in CBT with six of the intervention clinicians; half of these received at least six CBT manually-based sessions. Multiple barriers to CBT adoption and sustained use were identified by clinicians in qualitative interviews. CONCLUSION: Strategies to implement evidence-based interventions into routine clinical settings should include multi-method, pre-implementation assessments of the clinical environment and address multiple barriers to initial uptake as well as long-term sustainability.