This paper explores the equity issues in lower secondary education with specifi c focus on access and learning achievement in East Uganda. The study employs qualitative and quantitative approaches using school and individual level data. The results reveal that inequalities in both access and achievement are sensitive to school and family related factors including student age, household spending on education, education level of household head, latrine stances to student ratio as well as co-educational, urban and large schools. The qualitative investigation indicates inequality issues are real in the school communities. Though learning opportunities are available to both genders, there are voices of resentment regarding school environmental challenges such as inadequate sanitary facilities, ineffective counseling services, low parental participation in school gender activities as well as minimal protection that all pose danger to not only girl students especially, but also school property. The study finds that school stakeholders should have a sense of responsibility to equip schools with adequate facilities and improve safety as these measures can help to retain students, specifi cally girls, in schools. Collaboration of school managers with women's movements within school communities could show a strong infl uence in motivating girls' participation in schools as these approaches can break the negative gender stereotyping against girls.