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Abstract Tungiasis is a highly neglected tropical skin disease caused by the sand flea, Tunga penetrans. The flea burrows into the skin inducing a strong inflammatory response, leading to chronic pain and discomfort with potential impacts on quality of life. Few countries implement control efforts and there are few data on the impact of the disease to support policy decisions. We conducted a survey to determine the impact of tungiasis among primary school children across nine counties of Kenya. A total of 10,600 pupils aged 8 to 14 years were randomly selected from 97 primary schools and examined for tungiasis. Those with tungiasis (83) were interviewed with respect to their quality of life using a modified dermatological quality of life index. For these cases and 576 randomly selected controls, school attendance and exam scores for maths, English and science were collected from school records. Mixed effect ordered logistic and linear models were used to assess associations between disease status and impact variables. Compared to uninfected pupils, those with tungiasis missed more days of school (adjusted Incidence Rate Ratio (aIRR: 1.50, 95% CI: 1.03–2.21) and were less likely to receive a high score in maths (aOR 0.18, 95% CI: 0.08−0.40) and other subjects. Pupils with severe disease (>10 fleas) were five times more likely to experience severe pain and itching than those with mild disease (OR 5.0, 95% CI: 2.55−10.51) and a higher category of impact on their quality of life than those with mild disease (aOR 3.52, 95% CI: 1.22−10.17) when adjusted for covariates. This study has demonstrated tungiasis has a considerable impact on children’s lives and academic achievement, equivalent to other diseases. This indicates the need for integrated disease management for school-aged children to protect their physical and cognitive development and their future prospects. Author Summary Tungiasis is one of the most neglected tropical diseases (NTDs). It is caused by a flea which burrows into the skin of the feet. The neglect has resulted in large gaps in our knowledge of the disease, how to treat and prevent infection. This is partly due to a lack of appreciation for the impact the disease has on patients’ lives by health officials, policymakers and the research community. In this study we aimed to determine the impact on school children in nine counties of Kenya. We found evidence that children experience considerable pain and itching which affects their ability to attend school and to concentrate on their classes. They had lower exam scores in maths, English and science than uninfected children. This study has provided evidence that tungiasis is a disease that affects children just as much as other diseases and urgently needs more attention from researchers, donors, and policy makers. Integrating tungiasis into comprehensive disease management for school-aged children will protect their physical and cognitive development and their future prospects.