This paper reports an evaluation of the implementation of the School Health Policy (SHP) in Botswana schools. Historically, school health originated with a concern for the number of children being excluded from school owing to communicable diseases. In 1999, the three ministries, Ministry of Health, Ministry of Education and Ministry of Local Government, developed the Botswana School Health Policy and Procedures Manual. The school health services are organized at national, district and local levels. The purpose of the evaluation was to explore how school health services were delivered in schools in Botswana. Data on current practices on school health were collected using observations, field notes and interviews of various school personnel in 27 schools located in the Gaborone district, and surrounding villages using the assessment guide in the SHP. Content analysis was used to analyse the data. Several challenges to implementing the school health policy were identified, for example, lack of human resources, lack of equipment supplies, lack of health knowledge among teachers, as well as organizational problems. This has budgetary implications for Botswana at both central and district levels. Commitment of all stakeholders in all ministries concerned would also improve the implementation of school health services.