National indicators of higher education participation can obscure substantial geographic and gender inequalities within education systems. This study quantifies provincial and gender-based disparities in Nepal’s higher education system using reproducible mathematical and statistical techniques applied to University Grants Commission Education Management Information System data and the 2021 national census. Regional disparities were assessed using access ratios based on location quotients, an enrollment–population Lorenz curve, the Gini coefficient, and the Index of Dissimilarity, while gender disparities were examined through the Gender Parity Index (GPI), progression patterns across educational levels, and discipline-specific representation. The findings show that students from Bagmati Province participate in higher education at approximately 2.2 times the rate predicted by the province’s population share. Madhesh Province, rather than Karnali Province, recorded the country’s lowest relative access ratio at 0.40, indicating participation 60% below proportional representation. The provincial Gini coefficient was 0.31, numerically close to Nepal’s income Gini coefficient of 0.33, while the Index of Dissimilarity indicated that approximately one quarter of enrollment would need to be redistributed statistically across provinces for enrollment shares to correspond with population shares. The Gini coefficient declined modestly from 0.35 in FY 2019/20 to 0.31 in FY 2021/22. Nationally, the tertiary GPI increased from 0.26 in 1983 to 1.30 in FY 2023/24, representing a shift from pronounced male advantage to female-majority enrollment. However, substantial pipeline attrition persisted: female representation declined from approximately 57% at enrollment to 41% at the master’s level, approximately 16% at the MPhil and PhD levels, and less than 8% among university faculty in the most recent available data. Female representation was also markedly lower in Engineering (24.4%) and Sanskrit studies (14.5%). These findings demonstrate that national gender parity coexists with vertical, disciplinary, and regional inequalities. The study provides a reproducible framework for diagnosing these disparities and identifies province-by-gender disaggregation as an essential data-transparency priority for evaluating compounded disadvantage and informing equitable higher education policy.