Although Uganda was among the first sub-Saharan countries to introduce universal primary education in 1997, about 6% of children aged 9–11 had never been to school in 2014. An analysis of a 10% sample of the latest Uganda Population and Housing Census (2014) data set highlights striking spatial inequalities. We compare results from separate logistic regression analyses for the Karamoja subregion, the rest of the country, and the country as a whole. Our multilevel analyses show that the role played by household heads’ education and wealth in school enrolment emerges as a common factor. But while girls were significantly more likely to have never been enrolled in Karamoja and boys in the rest of Uganda, sex was not significant in the national model. Gendered expectations and constraints differ, which policies must consider. Our analysis questions the relevance of national models and therefore many national-level results in a context of high subnational heterogeneity.