
Children with disabilities while at school due to mainstreaming worldwide face many challenges. Mbale District, Uganda is not an exception. These challenges hinder their ability to participate actively in their education. The consequences are that they underperform or drop out of school all together. The many challenges faced include discrimination, negative attitude of teachers and normal fellow children, unsupportive roles of parents, lack of specialized services, unfriendly environment and infrastructure. The purpose of this study therefore was to examine the effect of discrimination on academic performance of children with disabilities in mainstreamed primary schools in Mbale District, Uganda. The study adopted a cross sectional survey research design. The population of the study included 3 Boards of Directors, 100 Headteachers. 1,600 Teachers, and 75,000 pupils. The study established that discrimination accounted for 94.9% of the variation in academic performance of children with disabilities. This means that discrimination in mainstreamed schools explained 94.9% of the children with disabilities in academic performance. The other 5.1% was due to other factors which were not the subject of this study. In essence, discrimination is a major factor in determining academic performance of children with disabilities in mainstreamed schools. The findings of this study are significant to stakeholders in Special Needs Education as they inform the way forward for successful inclusive education. Therefore; government should prioritize the needs of children with disabilities, refresher courses for teachers teaching children with disabilities, and the Directorate of the Education Standards should enhance standards in schools that handle children with disabilities.