INTRODUCTION: Evidence indicates children who suffer from ill-health are less likely to attend or complete schooling. Malaria is an important cause of morbidity and mortality in school-age children. However, they are less likely to receive malaria treatment at health facilities and evidence for how to improve schoolchildren's access to care is limited. This study aimed to evaluate the impact of a programme of school-based malaria case management on schoolchildren's attendance, health and education. METHODS: A cluster randomised controlled trial was conducted in 58 primary schools in Zomba District, Malawi, 2011-2015. The intervention, implemented in 29 randomly selected schools, provided malaria rapid diagnostic tests and artemisinin-based combination therapy to diagnose and treat uncomplicated malaria as part of basic first aid kits known as 'Learner Treatment Kits' (LTK). The primary outcome was school attendance, assessed through teacher-recorded daily attendance registers and independent periodic attendance spot checks. Secondary outcomes included prevalence of Plasmodium spp infection, anaemia, educational performance, self-reported child well-being and health-seeking behaviour. A total of 9571 children from standards 1-7 were randomly selected for assessment of school attendance, with subsamples assessed for the secondary outcomes. RESULTS: Between November 2013 and March 2015, 97 trained teachers in 29 schools provided 32 685 unique consultations. Female schoolchildren were significantly more likely than male to seek a consultation (unadjusted OR=1.78 (95% CI 1.58 to 2.00). No significant intervention effect was observed on the proportion of child-days recorded as absent in teacher registers (n=9017 OR=0.90 (95% CI 0.77 to 1.05), p=0.173) or of children absent during random school visits-spot checks (n=5791 OR=1.09 (95% CI 0.87 to 1.36), p=0.474). There was no significant impact on child-reported well-being, prevalence of Plasmodium spp, anaemia or education scores. CONCLUSION: Despite high community demand, the LTK programme did not reduce schoolchildren's absenteeism or improve health or education outcomes in this study setting. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov NCT02213211.