This study examined the influence of school van scheduling on the academic performance of primary school learners in Nansana Division, Wakiso District, Uganda. Specifically, the study assessed the relationship between total commute duration, number of pick-up and drop-off stops, van capacity utilization, and learners’ academic performance, as well as mechanisms for mitigating negative academic effects associated with prolonged school van schedules. A mixed-methods cross-sectional research design was adopted, integrating quantitative and qualitative approaches. The study was conducted in ten purposively selected private primary schools offering regular van transport services. A total of 341 participants were involved, including learners (P1–P7), parents/guardians, teachers, school administrators, van operators, and the Municipal Education Officer. Quantitative data were collected using questionnaires and academic records, while qualitative data were obtained through interviews, focus group discussions, and classroom observations. Quantitative data were analyzed using descriptive and group-level inferential patterns in SPSS, while qualitative data were analyzed thematically. Findings from both strands were triangulated to enhance validity. The findings revealed consistent group-level patterns indicating that long commute durations, frequent pick-up and drop-off stops, and high van occupancy levels were associated with learner fatigue, reduced alertness, diminished classroom engagement, and moderate academic performance. Overcrowding and discomfort, particularly in high-use vehicles, further compromised learners’ cognitive readiness and participation. Qualitative evidence highlighted stakeholder-proposed mitigation strategies, including route optimization, schedule adjustments, capacity regulation, and strengthened collaboration between schools, parents, and authorities. The study concludes that school van schedules are significant determinants of academic performance among primary school learners. It recommends learner-centered transport scheduling, enforcement of capacity guidelines, and policy-driven regulation of school transport systems to enhance academic outcomes.