This paper investigates the effects of intermittent screening and treatment of malaria on the health and education of school children in an area of low-to-moderate malaria transmission. A cluster randomized trial was implemented with 5,233 children in 101 government primary schools on the south coast of Kenya in 2010-12. The intervention was delivered to children randomly selected from classes 1 and 5 who were followed up twice across 24 months. Once during each school term, public health workers used malaria rapid diagnostic tests to screen the children. Children who tested positive were treated with a six-dose regimen of artemether-lumefantrine. Given the nature of the intervention, the trial was not blinded. The primary outcomes were anemia and sustained attention and the secondary outcomes were malaria parasitaemia and educational achievement. The data were analyzed on an intention-to-treat basis. Anemia in this setting in Kenya, intermittent screening and treatment, as implemented in this study, is not effective in improving the health or education of school children. Possible reasons for the absence of an impact are the marked geographical heterogeneity in transmission, the rapid rate of reinfection following artemether-lumefantrine treatment, the variable reliability of malaria rapid diagnostic tests, and the relative contribution of malaria to the etiology of anemia in this setting.