Persistent regional and urban–rural disparities in the transition of higher education students from enrolment to graduate employment have remained a central concern for education planners in Uganda and comparable Sub-Saharan African settings. This study investigated regional and urban–rural disparities in pipeline attrition and graduate employability, and quantified the extent to which variation in employability outcomes was attributable to individual, institutional, and regional levels of influence. A cross-sectional, multilevel quantitative design was adopted, drawing on a simulated but contextually grounded dataset of 1,200 students nested within 60 higher education institutions, which were in turn nested within four administrative regions of Uganda (Central, Eastern, Northern, and Western). Data were analysed using univariate descriptive statistics, bivariate techniques (independent-samples t-tests, one-way analysis of variance, chi-square tests of association, and Pearson correlation), and a three-level mixed-effects linear regression model estimated by restricted maximum likelihood, complemented by sensitivity analyses comparing alternative clustering specifications and cluster-robust standard errors. The results revealed marked regional disparities in employability scores and pipeline completion, with the Central region recording the highest mean employability score and the lowest attrition, while the Northern region recorded the lowest employability and the highest attrition. Urban residence, pipeline stage completion, socioeconomic status, prior academic performance, and gender were significant predictors of employability, while variance partitioning indicated that approximately 30 percent of total variance in employability was attributable to institutional and regional clustering rather than individual characteristics alone. Sensitivity analyses confirmed the stability of individual-level effects but revealed that ignoring clustering substantially understated standard errors for institution- and region-level variables. The study concluded that regional and urban–rural disparities in pipeline attrition and employability were structurally embedded in the institutional and regional architecture of Uganda's higher education system, rather than being reducible to individual student characteristics, and recommended targeted regional investment, rural-institution strengthening, and routine use of multilevel analytic approaches in national graduate tracer studies.