BACKGROUND: Following the COVID-19 pandemic, school closures were part of the global public health response to limit community spread of the virus. In recent times, there has been an emphasis on safe school re-opening. This concept is likely to differ between developed and developing country settings. There are however no published studies on barriers hindering safe school re-opening within developing country contexts. This study evaluates aspects of the school health program (SHP) in some selected Nigerian schools that might relate to the pandemic control during school re-opening. METHODS: In 2017, we conducted a cross-sectional survey of the SHP of 146 registered primary schools in Gwagwalada Area Council in Abuja, Nigeria. These schools provided services to about 54,562 students. We used direct observational methods and interviewer-administered questionnaires to assess the SHP of each school. We compare SHP characteristics that might relate to COVID-19 control in schools across government-owned (public) and privately-owned (private) schools using a pre-defined framework. RESULTS: Public school to pupil ratios was more than six times that of private schools. Only 6.9% of all surveyed schools employed qualified health personnel. Although 8 in every 10 schools conducted health talks for communicable disease control, the use of temporary isolation and school-based immunization were low at 1.4 and 2.7% respectively. Pipe-borne water access was present in 4 of 10 schools, with public schools having more limited access than private schools (p = 0.009). Similarly, less proportion of public schools had access to soap for handwashing (p < 0.001). Adequate classroom ventilation was present in 63% of surveyed schools, with private schools having more limited ventilation (p < 0.001). CONCLUSIONS: Overcrowding and infrastructural deficits within developing country contexts represent barriers to safe school re-opening during the COVID-19 pandemic. In these settings, there needs to be tailored and innovative strategies which consider local practical realities when designing the COVID-19 control programs during school re-opening.