Background: Endometriosis is one of the most common gynecological diseases that can lead to infertility. The aim of this quantitative, descriptive, and cross-sectional study was to analyze the prevalence and the annual nationwide health insurance treatment cost of endometriosis in Hungary in 2010 and 2019. Methods: The data used in this study were sourced from publicly funded, national, real-world datasets administered by the National Health Insurance Administration (NHIFA). The total number of cases of endometriosis in the Hungarian population was determined by ICD codes and all types of care. The total prevalence, age-specific prevalence, and annual health insurance expenditure by age group were evaluated. Results: The highest numbers of patients and prevalence (2010: 101.9/100,000 women; 2019: 197.3/100,000 women) were found in outpatient care. Endometriosis, regardless of its type, mainly affects patients in the 30–39-year age group (number of patients—2010: 6852; 2019: 11,821). The NHIFA spent a total of EUR 1,639,612 on endometriosis treatment in 2010 and EUR 1,905,476 in 2019. The average annual health insurance expenditure per capita was EUR 574 in 2010 and EUR 426 in 2019. There was a significant correlation between length of stay and mean age of patients in both years (2010 r = 0.856, p < 0.001; 2019 r = 0.877, p < 0.001). Conclusions: The number endometriosis cases is increasing. Early diagnosis and targeted treatment would reduce endometriosis symptoms and therefore improve patients’ quality of life and reduce health insurance costs. This would be helped by the establishment of endometriosis centers.