Facilitating mutually-beneficial educational activities between researchers and school students is an increasingly popular way for research institutes to engage with communities who host health research, but these activities have rarely been formally examined as a community or public engagement approach in health research. The KEMRI-Wellcome Trust Research Programme (KWTRP) in Kilifi, Kenya, through a Participatory Action Research (PAR) approach involving students, teachers, researchers and education stakeholders, has incorporated ‘school engagement’ as a key component into their community engagement (CE) strategy. School engagement activities at KWTRP aim at strengthening the ethical practice of the institution in two ways: through promoting an interest in science and research among school students as a form of benefit-sharing; and through creating forums for dialogue aimed at promoting mutual understanding between researchers and school students. In this article, we provide a background of CE in Kilifi and describe the diverse ways in which health researchers have engaged with communities and schools in different parts of the world. We then describe the way in which the KWTRP school engagement programme (SEP) was developed and scaled-up. We conclude with a discussion about the challenges, benefits and lessons learnt from the SEP implementation and scale-up in Kilifi, which can inform the establishment of SEPs in other settings.