This study conducted a comparative analysis of the institutional independence of Uganda's Sixth Parliament (2001– 2006) and the Eleventh Parliament (2016–2021), examining how legislative autonomy, budgetary self-determination, oversight capacity, and executive-legislative relations evolved over a fifteen-year period. Drawing on a mixedmethods design underpinned by neo-institutional theory and separation of powers doctrine, the study collected quantitative data from 186 purposively and randomly selected respondents comprising Members of Parliament, parliamentary staff, civil society representatives, and legal scholars. Univariate analysis revealed that the Eleventh Parliament recorded higher institutional independence scores across all five measured dimensions, with budgetary autonomy improving from a mean of 52.3 to 71.4 out of 100. Bivariate analysis using chi-square tests and Pearson correlation established statistically significant positive associations between parliamentary independence and legislative output (r = 0.74, p < 0.001), as well as between oversight autonomy and executive accountability ratings (r = 0.69, p < 0.001). Structural Equation Modelling (SEM) further confirmed that institutional independence (β = 0.72, p < 0.001) was a strong predictor of legislative effectiveness, mediated by recruitment autonomy (β = 0.48, p < 0.01) and budgetary control (β = 0.55, p < 0.001). The overall SEM model demonstrated acceptable fit (CFI = 0.94, RMSEA = 0.06, SRMR = 0.05). The findings underscore that while significant institutional gains have been achieved, structural vulnerabilities—particularly executive influence over parliamentary budgets and the appointment processes for senior parliamentary staff—continue to constrain full legislative independence. The study recommends constitutional entrenchment of parliamentary budgetary autonomy, a transparent and merit-based parliamentary service commission, and strengthened inter-institutional accountability mechanisms to consolidate democratic governance in Uganda.