This study examined the relationship between discipline as a form of self-control and STEM academic performance among secondary school students in Uganda, with specific reference to the national STEM Education Policy. Grounded in self-determination theory and Vygotsky's socio-cultural framework, the study sought to determine how student self-control, discipline, and school-level policy exposure collectively influenced STEM outcomes across different school types and geographic settings. A cross-sectional, mixed-methods design was employed, drawing on a stratified random sample of 1,200 students from 60 secondary schools across Uganda's four regions. Quantitative data were collected using structured questionnaires measuring self-control, discipline, and STEM performance, while qualitative insights were gathered through focus group discussions and key informant interviews. Descriptive statistics, Pearson bivariate correlations, ordinary least squares regression, and three-level hierarchical linear modelling (HLM) were applied to analyse the data. Findings revealed that self-control (β = 0.241, p < 0.001) and discipline scores (β = 0.187, p < 0.001) were strong and statistically significant predictors of STEM performance even after controlling for school-level and regional factors. The intra-class correlation in the null model was 0.234, confirming that 23.4% of the variance in STEM scores was attributable to school-level differences, which reduced to 16.7% in the full model after accounting for policy exposure, school type, and urbanisation. Private urban schools consistently outperformed government rural schools, pointing to structural inequalities that undermine the equitable aims of Uganda's STEM policy. Policy exposure was itself a positive predictor of proficiency (β = 0.323, p < 0.001), suggesting that sustained and quality implementation of the STEM policy has measurable academic dividends. The study concluded that discipline and self-control are not merely moral virtues but are academically consequential competencies whose cultivation should be embedded in Uganda's STEM policy framework. Recommendations include targeted teacher-training on discipline-integrated pedagogy, resource equalisation across rural and urban schools, and a formal monitoring framework for STEM policy implementation.