The prevalence of autism spectrum disorder in South Africa is unknown and, to date, very little research has been performed within school systems that could inform the rates, distribution and profile of needs of children with autism spectrum disorder in education. We performed a comprehensive database search of all children with autism spectrum disorder in the formal education system in the Western Cape province of South Africa and compared the findings with population demographic expectations of the province. From a population of 1,154,353 children attending schools in the province, a total of 940 children with a diagnosis of autism spectrum disorder were identified, representing a rate of 0.08%. The male: female ratio was 5.5:1. There was a significant difference in the self-reported racial and language composition of the autism spectrum disorder sample compared with the Western Cape demographics where a higher proportion of children with autism spectrum disorder were from White racial groups and English-speaking homes. Eighty-nine percent of children with autism spectrum disorder were in Special Schools and only 10% were in Ordinary/Mainstream Schools. Most of the children (83%) attended schools in the City of Cape Town and only 17% in rural areas. Co-occurring intellectual disability was reported in 22.2% of the population, attention-deficit/hyperactivity disorder in 2.6% and epilepsy in 0.7%. Data showed a 76.03% increase in autism spectrum disorder in schools between 2012 and 2016, with an average increase of 15.18% per year. Findings suggested an under-representation of autism spectrum disorder in schools and an under-identification of co-occurring conditions. Results indicate that despite being one of the better-resourced provinces in South Africa, the Western Cape is not equipped to identify and meet the culturally and linguistically diverse needs of its communities. We propose strengthening of educational systems for children with autism spectrum disorder in the Western Cape, and similar investigations in other South African provinces. Lay abstract There is very little information about autism spectrum disorder in South Africa and not much is known about children with autism spectrum disorder and their educational needs. In this study, we searched for all children with autism spectrum disorder attending schools in the Western Cape province of South Africa and compared our findings with the profile of people living in the province. We found fewer children with autism spectrum disorder in schools than expected (0.08%) and co-occurring conditions (intellectual disability = 22.2%, attention-deficit/hyperactivity disorder = 2.6% and epilepsy = 0.7%) were reported at lower rates. More children were from White racial groups and from English-speaking homes compared with the Western Cape population demographics. Most of the children (89%) attended schools for children with Special Educational Needs and only 10% were in Ordinary/Mainstream schools. Eighty-three percent attended schools in urban areas and 17% in rural areas. There was a 76.03% increase in children with autism spectrum disorder in schools between 2012 and 2016. Our findings support the need for better identification and reporting of children with autism spectrum disorder in the education system. We propose urgent review and strengthening of education systems for children with autism spectrum disorder in the Western Cape province and in other parts of South Africa.