IntroductionChildren attending school whilst unwell, known as school-based presenteeism, results in negative impacts on education and mental and physical health. We aimed to identify the risk factors for this behaviour.MethodWe conducted a systematic search of five databases (11 July 2022) using words associated with school (e.g., school and childcare) and presenteeism (e.g., presenteeism and sick leave). The studies are synthesised according to the risk factors associated with school-based presenteeism and are grouped into themes by related topics.ResultsOur review included 18 studies, with quantitative, qualitative, and mixed-method study designs. Children, parents, and school staff reported past incidents and intentions for future presenteeism. We identified five themes from these reports: perceptions about the illness / signs and symptom(s); children’s characteristics; children’s and parents’ motivations and attitudes towards school; organisational factors; and school sickness policy. Increased risk of school-based presenteeism was commonly linked to symptoms that were perceived low in severity and unidentifiable, children with a high school absence record, disbelief in children’s illness, unsupportive employers, vague school policies and financial consequences.ConclusionsSchool-based presenteeism is complex due to the competing interests of the multiple individuals involved, such as children, parents, and school staff. Sickness policies need to include clear and specific guidance about illness and the signs and symptoms of diseases and should be communicated to all relevant individuals to mitigate against discrepancies in how the policy is interpreted. Furthermore, parents and school staff need support, such as financial and childcare, to be able to manage children when they are unwell.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40359-023-01207-1.