Extramammary Paget’s disease (EMPD) is a rare intraepithelial adenocarcinoma that significantly impacts quality of life due to its chronic and symptomatic nature. A population-based study using data from China’s Urban Employee and Resident Basic Medical Insurance in 2016 aimed to assess EMPD prevalence and its demographic patterns in China, where no national data previously existed. The study identified 84 cases, revealing a crude prevalence of 0.04 per 100,000 population, with regional variations ranging from 0.01 in North/Northeast China to 0.08 in Southwest China. The condition was more common in males (0.05) than females (0.03) and most prevalent among individuals aged 70–79 (0.28). This prevalence is notably lower compared to Western countries, and the Chinese patients were generally younger with a significant male predominance. Further research is needed to explore the underlying mechanisms of EMPD.