School transportation significantly influences learners' educational experiences in urban Uganda. The number of pick- up and drop-off stops affects travel duration, fatigue levels, and ultimately academic performance. This study examined how transport stop frequency impacted learner outcomes in Nansana Division, Wakiso District. A cross- sectional survey design was employed with 341 participants including learners, parents, teachers, and school administrators from 12 primary schools in Nansana Division. Data were collected through structured questionnaires, academic records analysis, and focus group discussions. Statistical analysis included correlation tests, regression analysis, and descriptive statistics using SPSS version 26. The study revealed a significant negative correlation (r = - 0.614, p < 0.001) between the number of transport stops and academic performance. Learners who experienced 1-3 stops achieved mean scores of 78.4%, while those with 8+ stops averaged 62.3%. Extended travel time (exceeding 90 minutes) was associated with increased absenteeism (24.7%) and reduced concentration levels (68.9% reported fatigue). The number of pick-up and drop-off stops substantially affected academic performance among primary school learners in Nansana Division. Multiple stops increased travel duration, physical exhaustion, and reduced study time, consequently diminishing learner achievement. Schools and transport providers should optimize routes to minimize stops, establish maximum stop thresholds, and implement staggered scheduling systems to reduce learner travel burden.