Children in Sub-Saharan Africa (SSA) experience high rates of mental health problems, and the region has limited access to mental health resources and research capacity to address the needs. Despite the success of numerous evidence-based interventions (EBIs) and emerging methodology from the field of implementation science for addressing child mental health needs, most EBIs and implementation science methodology have not been applied in SSA contexts. The SMART-Africa Center aims to address these child welfare, mental health, services, and EBI implementation research gaps by establishing a regional trans-disciplinary collaborative center and studying strategies to strengthening mental health system and implementation research capacity. Our paper describes the overall framework and strategies that SMART-Africa team developed to strengthen capacity in three SSA countries (Ghana, Kenya, and Uganda) while focusing on its contextualization for the Kenyan school-community mental health settings. Methods to document the progress and impacts are also described. The design of the system and research strengthening activities is guided by a SMART-Africa Capacity Building framework. Two areas of capacity are focused. Mental health system capacity focuses on building political wills, leadership, transdisciplinary partnership, and stakeholders' global competency in evidence child mental health policy, intervention, and service implementation research. Implementation research capacity building focuses on building researchers' implementation research competency by carrying out an EBI implementation research (using a Hybrid Type II effectiveness-implementation). For illustration purpose, we describe how the system strengthening strategies has been applied in Kenya, and how the mixed methods design applied to assess the value and impacts of the capacity building activities. Feedback data and evaluation data collection using qualitative and quantitative methods for both areas of capacity building are still ongoing. Data will be analyzed and compared across countries in 2020-2021. Our work has shown some feasibility of applying the theory-guided system strengthening model in improving child mental health service system and research capacity in one of the three SMART-Africa partnering countries. Our mental health landscape and resource mapping in Kenya also illustrated that capacity building in SSA countries involved complex dynamic, history, and some overlap efforts with multiple partnerships, and these are critical to consider in training activity and evaluation design.