Literature indicates a high prevalence and burden of mental illness in youths world-wide, which may be even higher in low- and middle-income countries (LMIC), such as South Africa and Zambia. Additionally, there is a lack of knowledge regarding youth depression amongst many primary health care (PHC) practitioners. The principal goal of the MEGA project is to provide youth with better access to mental health services and appropriate care, by developing a mental health screening mobile application tool to be used in PHC settings in South Africa and Zambia. In this study, we will use a mixed methods multi-center study design. In phase one, we will investigate the mental health literacy of PHC practitioners to identify areas in need of development. Based on the needs identified, we will develop and test a mobile health application to screen for common youth mental health problems in phase two. In phase three, we will implement and evaluate a tiered education and training program in the use of the m-health application. In the final phase, we will evaluate the acceptability and feasibility of the m-health application in PHC centres across South Africa and Zambia. Evidence suggests that PHC practitioners should routinely consider mental illness when assessing youth. However, common psychiatric disorders remain largely undetected and untreated in PHC settings. By identifying limitations in PHC workers knowledge with regard to youth mental health, we aspire to improve the depression care provided to youth in Southern Africa and Zambia by developing and implementing a locally relevant m-health application.