School-age children bear an under-appreciated burden of malaria and are a key reservoir for the spread of P. falciparum. We conducted school-based cohort studies to measure the impact of treating students with positive malaria rapid diagnostic tests on subsequent gametocyte, the parasite stage required for human-to-mosquito transmission, prevalence and density. We concomitantly quantified the proportion of gametocyte burden in school-age children and compared it to that of other age groups in household-based surveys in the school catchment area. Treatment reduced the prevalence and density of gametocytes by 79% and 89%, respectively. Half of all gametocyte-containing infections were detected in school-age children. We estimated that school-based malaria treatment could reduce overall gametocyte prevalence in the community by 26% and 34% in the rainy and dry seasons, respectively. These results suggest that school-based malaria treatment could further decrease the burden of malaria in areas where malaria has remained entrenched despite current control measures.