This is a replication dataset for the manuscript titled: "National prevalence and risk factors for tungiasis in Kenya." Data set of 59 variables for 21,466 primary school pupils collected when examining them for tungiasis as part of a national survey to determine the national prevalence of the disease. The variables include whether a pupil was infected or not, how many fleas they had embedded in their skin and the associated symptoms on the feet to assess the intensity and severity of infection.