Globally, notable emphasis is currently being placed on improving access to and acceptance of sanitation in schools as part of the drive towards achieving the United Nations Sustainable Development Goal 6. However, the importance of sustaining effective cleaning of latrines in schools remains an under-emphasized and under-researched topic, with serious negative consequences for the health of school-aged children in low-income settings. In this Perspective, we summarize the limited existing literature on the impacts of unclean latrines in schools on aspects of child health, and the methods that have been trialled to achieve sustainable school latrine cleaning programmes. We highlight research needs and propose a new approach to school-led total sanitation, with the aim of moving towards a world in which no child gets sick because of the unhygienic state of the toilets in their schools.