This article describes the findings of a qualitative study on knowledge, beliefs, attitudes, and practices towards children with spina bifida and hydrocephalus in four regions of Uganda. Focus group discussions and semi-structured interviews were held with parents of children with spina bifida and hydrocephalus, policy-makers, and service providers. Our findings describe how negative knowledge, beliefs, attitudes, and practices create barriers to treatment and inclusion of children with spina bifida and hydrocephalus and their parents in Uganda. The findings show how knowledge, beliefs, attitudes, and practices evolve over time, are both similar and differ in the various regions, and become more conducive towards accessing treatment and achieving inclusion. Sensitisation and early intervention including parents and service providers in dissemination of knowledge, rehabilitative care to set the trend for positive change and support, as well as longitudinal studies of children with spina bifida and hydrocephalus and their parents are recommended.