Podoconiosis is a type of tropical lymphedema that is clinically distinguished from lymphatic filariasis (LF) because it is ascending and commonly bilateral but asymmetric. The disease is a result of a genetically determined inflammatory reaction to long-term exposure to mineral particles in irritant red clay soils derived mainly from volcanic soils. We conducted the first nationwide mapping of the prevalence and risk factors of podoconiosis in Kenya. We performed a population-based cross-sectional survey to determine the national prevalence of podoconiosis and included 6,228 individuals from 48 villages in 24 sub-counties across 15 counties. Participants answered a questionnaire about the history of symptoms compatible with podoconiosis, received a point-of-care antigen test, and underwent a physical examination if they had lymphedema. A confirmed case of podoconiosis was defined as a case in a resident of the study village who had lower limb bilateral and asymmetric lymphedema lasting more than 1 year, negative test results for Wuchereria bancrofti antigen, and other causes of lymphedema ruled out. Of all the individuals surveyed, 89 had lymphedema; of those, 16 of 6228 (0.3%; 95% confidence interval [CI], 0.1–0.5) were confirmed to have podoconiosis. A high prevalence of podoconiosis was found in western (Siaya, 3.1%; Busia, 0.9%) and central (Meru, 1.1%) regions, and a low prevalence was observed in northern (Marsabit, 0.2%), eastern (Makueni, 0.2%), and coastal (Tana River, 0.1%) regions. The identified risk factors were age 56 years or older (adjusted odds ratio [aOR], 5.66; 95% CI, 2.32–13.83; P < 0.001) and rarely wearing shoes (aOR, 18.92; 95% CI, 4.55–78.71; P < 0.001). These results indicated that the podoconiosis prevalence is low and localized in Kenya; therefore, elimination is achievable if appropriate disease prevention, management, and behavioral strategies are promoted.