Early pregnancy constitutes one of the most pervasive yet structurally embedded barriers to girls' secondary education in Uganda, operating through intersecting social, economic, and institutional mechanisms that collectively sustain gender inequality. This study examined the role of early pregnancy as a mechanism of female educational exclusion in Ugandan secondary schools, with a specific focus on the prevalence of school dropout attributable to pregnancy, the socio-economic and institutional factors that mediate the pregnancy-dropout relationship, and the effectiveness of existing re-entry policies and school-based support systems in facilitating academic continuation. A cross-sectional quantitative research design was employed, utilizing a structured questionnaire administered to a sample of 500 female secondary school students and recent school leavers from 20 purposively selected secondary schools across rural and urban districts in Uganda. Data were analysed using univariate descriptive statistics, bivariate chi-square tests, and binary logistic regression. The findings revealed that 40.2% of respondents reported a history of pregnancy, of whom 87.2% had dropped out of school. Early pregnancy was the strongest independent predictor of school dropout (Adjusted OR = 28.7; 95% CI: 14.3-57.6; p < 0.001), followed by lack of access to school re-entry policies (Adj OR = 31.4; 95% CI: 17.2-57.4; p < 0.001). Rural residence, low household income, and low paternal education further compounded dropout risk. Re-entry rates were dismally low (22.1%) and strongly associated with access to financial support, parental encouragement, and teacher attitudes. The study concluded that early pregnancy functions not merely as a biological event but as a socially and institutionally amplified mechanism of educational exclusion, whose effects are disproportionately borne by girls in resource-constrained and rural settings. The study recommends strengthening national school re-entry policies, scaling up multi-sector socio-economic support programmes for pregnant and parenting learners, and implementing comprehensive sexuality education integrated into the formal secondary school curriculum to address the root causes of adolescent pregnancy and its educational consequences.