This study examined the influence of inclusive school management practices on students’ academic performance in Science, Technology, Engineering and Mathematics (STEM) subjects in public day secondary schools in Bugesera District, Rwanda. Specifically, the study assessed the influence of inclusive leadership, student support systems, equitable resource distribution, and teacher support programs on STEM performance. The study adopted a descriptive research design combining quantitative correlational and qualitative descriptive approaches. From a target population of 522 respondents (476 students, 32 teachers, and 14 headteachers) drawn from 14 public day secondary schools, a sample of 227 respondents was determined using the Yamane formula and selected through stratified, simple random, and purposive sampling. Data were collected using structured questionnaires and interview guides and analysed descriptively and inferentially using IBM SPSS version 28.0. The findings show that inclusive school management practices moderately influenced STEM performance, with strong statistically significant positive correlations among all constructs (r = .746 to r = .960, p < .01) and a regression model in which inclusive management practices explained 91.4% of the variance in academic performance (R = .963, R² = .914, F = 103.907, p < .001). Implementation gaps, notably weak student representation, limited teacher involvement in academic planning, inadequate and poorly maintained STEM resources, and insufficient in-service training, constrained the full benefit of otherwise inclusive intentions. The study recommends strengthening participatory leadership, improving STEM resource provision and maintenance, institutionalising continuous professional development, and integrating comprehensive student support systems.