School health has been identified as a neglected aspect of primary health care in Ghana, leading to compromised health, well-being and life satisfaction among students. To address this concern, this study identified the barriers hindering the implementation of school-based health programs in Ghana. It employed a qualitative approach, including 116 respondents who participated in interviews. The collected data were analyzed using thematic analysis with the aid of NVivo software. In line with the research objective, findings show that the implementation of school-based health programs faces several teething challenges that serve as barriers to the success and sustainability of the programs. These barriers included resource constraints; a lack of adequate parental and community participation and a lack of adequate collaboration between stakeholders' management and leadership issues, governance issues and political issues. The findings from the study have a relevant and innovative contribution to achieving good health and well-being and quality education as part of the 2030 Agenda for Sustainable Development Goals and shaping primary healthcare management in the context of a developing country. It recommends that policymakers and health practitioners pay special attention to school-based health programs as a key strategy for primary health care management in developing countries.