Purpose: Health education that integrates community participation is essential for malaria control. However, children's participation is not generally as active as that of adults, thus turning children into recipients, as opposed to partners in malaria control. The purpose of this paper is to develop a better understanding of how children can transform from mere recipients to active partners in malaria control efforts, by exploring the implementation of a school health education program in Uganda. Design/methodology/approach: A qualitative multi-case study involving six schools where the health education program was implemented was undertaken, using six focus group discussions with 72 school children and respondent interviews with 14 teachers and district health promotion staff. Findings: Children acted as health messengers, offered peer support and engaged in environmental management to minimize mosquito breeding. The benefits of the school malaria program included increasing access to malaria information, boosting malaria knowledge, improving children's self-esteem and their skill as health educators. However, implementation was undermined by hostility from adults, inadequate time and tight school schedules, which should be addressed in future malaria programs. Practical implications: The findings suggest that children can play an important role in malaria programs. Therefore, programs should be sufficiently structured to facilitate children's participation. Practitioners should be encouraged to be conscious of the applicability of the health promoting school approach to malaria control. Originality/value: This research facilitated a more comprehensive understanding of the role children can play in malaria control, thus providing a basis for their involvement in malaria programs. It also adds to a relatively scarce area of literature on the school health-malaria control nexus.