Background Child and adolescent mental health problems account for a significant proportion of the local and global burden of disease and is recognized as a growing public health concern in need of adequate services. Studies carried out in Kenya suggest a need for a robust service for the treatment, prevention, and promotion of child and adolescent mental health. Despite a few existing services to provide treatment and management of mental health disorders, we need more knowledge about their effectiveness in the management of these disorders. This paper describes a study protocol that aims to evaluate the process and outcomes of psychotherapies offered to children and adolescents seeking mental health services at the Kenyatta National Hospital in Kenya. Methods This study will use a prospective cohort approach that will follow adolescent patients (12-17 years of age) receiving mental health services in the youth clinics at the Kenyatta National Hospital for a period of 12 months. During this time a mixed methods research will be carried out, focusing on treatment outcomes, therapeutic relationship, understanding of psychotherapy, and other mental health interventions offered to the young patients. In this proposed study, we define outcome as the alleviation of symptoms, which will be assessed quantitatively using longitudinal patient data collected session-wise. Process refers to the mechanisms identified to promote change in the adolescent. For example, individual participant or clinician characteristics, therapeutic alliance will be assessed both quantitatively and qualitatively. In each session, assessments will be used to reduce problems due to attrition and to enable calculation of longitudinal change trajectories using growth curve modeling. For this study, these will be referred to as session-wise assessments. Qualitative work will include interviews with adolescent patients, their caregivers as well as feedback from the mental health care providers on existing services and their barriers to providing care. Conclusion This study aims to understand the mechanisms through which change takes place beyond the context of psychotherapy. What are the moderators and through which mechanisms do they operate to improve mental health outcomes in young people?