Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication and social interaction as well as repetitive behaviors and restricted interests. The genetic mechanism underlying ASD is as complex and heterogeneous as the clinical presentation of the disorder itself. Megalencephaly-Capillary Malformation Syndrome (MCAP) is a rare genetic disorder that is associated with mutations in the ADGRV1 and PIK3CA genes. To the best of our knowledge, there is only one case report in the literature that documents the coexistence of MCAP and ASD. In this case study, we present the case of a 14-year-old girl diagnosed with both ASD and MCAP who was admitted to our clinic. Diagnosing ASD in patients with genetic syndromes can be challenging due to pre-existing cognitive and medical issues. This case underscores the importance of regular child psychiatry follow-ups for children with genetic syndromes to ensure timely and accurate diagnosis of ASD.