 While malaria represents one of the main health problems afflicting schoolchildren, the evidence base for policy development and programme implementation for school-based malaria control remains inadequate. A recent study in western Kenya showed that delivering intermittent preventive treatment IPT to schoolchildren improved rates of anaemia and classroom concentration, but did not improve school performance. This study aims to i investigate the impact of malaria prevention using a strategy of periodic screening using malaria rapid diagnostic tests and treatment positives using artemether-lumefantrine AL on health and education among schoolchildren and ii determine the interaction between health and improved literacy instruction. The study hypothesis is that that school-based malaria prevention will reduce rates of anaemia or improve educational outcomes in Kenyan schoolchildren, when compared to comparison schools. In addition, a programme of training for primary school teachers to improve literacy instruction will improve literacy rates and there will be no interaction between the malaria intervention and the education intervention, such that learning will not be improved when teaching is effective and children are healthy. The study will be undertaken in 101 randomly selected primary schools in Kwale District. The malaria intervention consists of screening all children using rapid diagnostic tests RDTs for malaria. Children with or without clinical malaria symptoms found to be RDT-positive will be treated with AL according to national guidelines. Screening and treatment will be administered by district public health staff once a school term, observed by the evaluation research team. This intervention has been changed from IPT due to the withdrawal of amodiaquine in Kenya. The education intervention includes a programme of training for primary school teachers to improve literacy instruction. The study is designed to detect a 25 reduction in anaemia and an improvement of 0.2 standard deviations in mathematics and literacy tests. Additional outcomes will also be measured including malaria parasitaemia, classroom attention and school attendance. Cost-effectiveness and community acceptability of the interventions will be assessed. Anaemia and educational outcomes will be assessed before interventions and 12 and 24 months later. Malaria parasitaemia using blood slides will only be assessed at follow-up. 