This study examines the structural dynamics, disciplinary concentration, and distributional inequality of Master's education at the University of Ibadan (UI), Nigeria's premier research university, over a twenty-year period (2005–2025). Using a complete administrative dataset of 59,040 Master's degree graduates spanning two analytically distinct structural regimes, Phase I: Classic Expansion (2005–2018; N = 42,133) and Phase II: Reconfiguration and Exogenous Shock (2019–2025; N = 16,907), the study employs a multi-method quantitative framework integrating the Herfindahl–Hirschman Index (HHI), Theil T Index, Compound Annual Growth Rate (CAGR) analysis, and shift share decomposition. Structural break testing confirms 2019 as the boundary of a systemic reconfiguration coinciding with COVID-19 disruption (2020: N = 219) and institutional restructuring. The findings reveal a persistent core–periphery architecture in which Social Sciences, Education, and Science collectively command between 52% and 63% of institutional output across both phases, even as new disciplinary actors, particularly Multidisciplinary Studies, UI School of Business, and Public Health, emerge in Phase II. Institutional concentration decreased significantly (average HHI: Phase I = 0.1515; Phase II = 0.1370), and inequality declined (average Theil T: Phase I = 0.620; Phase II = 0.471); however, these improvements mask both COVID-induced volatility and a structural shift away from Agriculture and toward market-responsive professional programmes. Shift–share WAMDEVIN-IJMDC decomposition reveals that Technology (CAGR: 9.10%), Medical/Health Sciences (CAGR: 5.82%), and Science (CAGR: 2.98%) are the principal competitive gainers, while Social Sciences (CAGR: −3.50%) and Education (CAGR: −0.57%) experienced competitive erosion despite their continued volumetric dominance. For Social Sciences, the competitive effect of −510.6 is particularly striking: the faculty not only underperformed the institutional growth benchmark but experienced an absolute decline in output (from 630 to 309 graduates). The study concludes that Master's education expansion at UI has been structurally segmented rather than uniformly inclusive, driven more by professional market demand than by deliberate national human capital strategy. Consequently, it proposes a differentiated postgraduate investment framework grounded in competitive positioning evidence.