OBJECTIVES Rwanda was the first country in Africa to introduce the human papillomavirus (HPV) vaccine. This was achieved through multi-year school-based campaigns. Our study evaluated the impact of the HPV vaccine introduction on the country's immunisation programme and health system. METHODS Thirty key informants were interviewed at national and district levels, and in participating schools. Twenty-seven health facilities completed a questionnaire exploring the effects of the new vaccine introduction on six health system building blocks, as defined by the World Health Organization. Routine service activity data were collected during a 90-day period around the introduction. RESULTS Routine vaccination activities were not disrupted during the delivery, likely due to a strong Expanded Program on Immunization, appropriate planning and a well-resourced operation. Opportunities were seized to co-deliver other interventions targeted at children and adolescents, such as health promotion. Collaboration with the Ministry of Education was strengthened at national level. Although there were some temporary increases in staff workload, no major negative effects were reported. CONCLUSION Despite its delivery through school-based campaigns, the HPV vaccine integrated well into the immunisation programme and health system. The introduction had no major negative effects. Some opportunities were seized to expand services and collaborations.