Competency-Based Curriculum (CBC) has gained growing traction as a transformative framework for restructuring higher education systems across sub-Saharan Africa, yet its application within Ugandan undergraduate institutions remains fragmented and underexplored. This study examined the extent to which CBC principles were integrated into training, assessment, and curriculum delivery practices across selected Ugandan universities, and assessed the factors that predicted student academic outcomes under a CBC framework. A cross-sectional survey research design was employed, drawing on a stratified random sample of 385 respondents comprising 210 undergraduate students and 175 lecturers from eight universities, spanning public, private, technical, and faith-based institutions. Data were collected using validated Likert-scale questionnaires and analysed through a three-tiered statistical approach: univariate analysis to characterise distributional patterns across all study variables; bivariate analysis—including Pearson correlations and one-way ANOVA—to examine associations and group differences; and two-level multilevel modelling to partition outcome variance between individual and institutional levels while controlling for confounding. Findings revealed moderate-to-low mean scores across CBC implementation dimensions, with Curriculum Delivery Quality (M = 3.29, SD = 0.72) and Instructor Training (M = 2.98, SD = 0.93) emerging as areas of particular concern. Correlation analysis established statistically significant and positive associations between CBC Awareness, Assessment Alignment, and Student Academic Outcomes (r = .559, p < .001 and r = .612, p < .001, respectively). One-way ANOVA indicated significant differences in CBC delivery across institution types (F(3, 381) = 11.47, p < .001, η² = .083) and programme categories (F(4, 380) = 9.76, p < .001, η² = .093). The multilevel model explained 54% of variance in student outcomes (Conditional R² = 0.54), with Instructor Training Score (β = 0.43, p < .001) and Institutional Support Index (β = 0.27, p = .015) identified as significant institutional-level predictors. These results underscore the urgency of structured CBC professional development for lecturers, standardised institutional policy frameworks, and sustained investment in pedagogical infrastructure to optimise the impact of CBC in Ugandan undergraduate education.