Endometriosis is a disease that is often diagnosed late and that may lead to significant reduction in quality of life and serious complications (e.g., infertility). We aimed to assess the prevalence and the annual, nationwide health insurance treatment cost of endometriosis in Hungary using a quantitative, descriptive, cross-sectional method, focusing on the year 2019. We used claims data obtained from the Hungarian National Health Insurance Fund Administration (NHIFA). Patient numbers, total and age-specific prevalence, annual health insurance expenditure, and the distribution of costs across age groups were determined. The NHIFA spent a total of HUF 619.95 million (EUR 1.91 million) on endometriosis treatment. The highest number of patients and prevalence (10,058 women, 197.3 per 100,000) were found in outpatient care. In acute inpatient care, prevalence was substantially lower (23.5 per 100,000). Endometriosis, regardless of its type, affects 30–39-year-olds in the highest number: 4397 women (694.96 per 100,000) in this age group were affected in 2019. The average annual health insurance expenditure per capita was EUR 189.45. In addition to early detection and diagnosis of endometriosis, it is of pivotal importance to provide adequate therapy to reduce costs and reduce the burden on the care system.