Childhood injuries remain understudied in Uganda. The objective of this study was to determine the extent, nature and determinants of school-related childhood injury risk in north-western Uganda. A cohort of 1000 grade fives from 13 elementary schools was followed-up for one term. Survival and multi-level modelling techniques compared the risk rates across gender, schools and locations. Childhood injuries are common in north-western Uganda. Most of them occur during travel, breaks, practical classes and gardening, while walking, playing, learning and digging. Most injuries result from collisions with objects, sports and falls. Two-thirds of children receive first aid and hospital care. Times to injury were 72.1 and 192.9 person days (p = 0.0000). Gender differences in time to event were significant (p = 0.0091). Girls had better survival rates: cumulative prevalence of childhood injury was 36.1%; with significant gender differences (p = 0.007). Injury rate was 12.3/1000 person days, with a hazard ratio of 1.4. Compared to girls, boys had a 37% higher injury rate (p = 0.004). Rates varied among schools. Associated factors include sex and school. Rural-urban location and school differences do influence childhood injury risk. Childhood injuries are common: the risk is high, gender- and school-specific. Determinants include gender and school. Location and school contexts influence injury risk.