Four health promoting (HP) schools were established in rural communities in Uganda by a joint Ugandan/Canadian university team. The model was based on a successful Canadian health promotion initiative designed to address poor oral health in Aboriginal children in rural and remote communities. Careful situation analysis, orientation of partner schools and collaborative development of educational materials and evaluation methodology preceded implementation. The intervention had three elements: inclusion of health topics by teachers in regular classroom activities; health education delivered by the university team to reinforce key educational concepts; and daily in-school tooth brushing to develop healthy practices. All children entering Grade 1 at four schools were recruited for 4 years; evaluation included year 1 pre-intervention and annual end-of-year data collection of quantitative and qualitative measures. Principal findings at 4 years included: an increase from baseline in the original cohort (n = 600) in those brushing at least once daily (p < 0.05) and before bed (p < 0.05); improved oral health (less ‘bad breath’, pain and absences for emergency dental treatment); more comprehensive health knowledge. Other positive observations were change in the schools’ health culture; children sharing new health knowledge and advocating for health practices learned; and evolution of health promotion activity to address other community-identified issues following success with the initial oral health component. University faculty and students learned from participation in programme delivery and community-based educational opportunities. School-based health promotion using this oral health model was readily accepted, implemented, sustained and evaluated; all communities took ownership, and all schools continue their programmes. Addressing oral health through HP schools is novel in Africa, and several lessons learned are of potential value for similar health promotion initiatives in sub-Saharan Africa.