Introduction: Young people’s health concerns represent major challenges for healthcare systems worldwide. In Benin, we are witnessing a rise in risky behaviors in young people (drug use, physical violence, premature pregnancies), despite the intervention of school nurses. Objective: To describe and understand the practices of school nurses in promoting the health of secondary school pupils in the Republic of Benin. Method: A multiple-case study was conducted in 2 departments of Benin. Hybrid analyses were based on semi-structured interviews (n = 35) with high school and middle school directors (n = 14), school nurses (n = 14), managers from the Ministry of Health (n = 4) and the Ministry of Technical Secondary Education and Vocational Training (n = 3), supplemented by observations and field notes. King’s systems model guided data collection and analysis. Results: Gaps in health promotion nursing practices include 1) the low level of organization of promotional activities, 2) insufficient availability of human and material resources, 3) insufficient knowledge of health promotion in schools, and 4) lack of coordination of school nurses’ activities. Discussion and Conclusion: Health promotion within the school setting remains unevenly implemented. Deficiencies in training, organizational structure, and the availability of human and material resources significantly constrain the performance of school nurses, thereby revealing a persistent structural vulnerability within the school health system across the Beninese departments included in this study.