Intellectual disabilities (ID) are neurodevelopmental disorders characterized by deficits in intellectual functioning and adaptive behavior which includes conceptual, social and practical skills. 1 out of 4 individuals with ID have co-existing autism spectrum disorder (ASD). Recently, cell therapy has shown great potential in management of ID with ASD due to their ability to address the underlying pathophysiology via immunomodulation and synaptogenesis. We administered autologous bone marrow mononuclear cells intrathecally in a 20-year-old male patient diagnosed as ID with ASD. Over 3 years follow up, there were no adverse events and along with symptomatic improvements, IQ scores improved from 46 to 56 and scores on ISAA improved from 134 to 70. Comparative positron emission tomography–computed tomography brain showed improved metabolism in bilateral frontal, temporal cortices and cerebellum. Autologous bone marrow mononuclear cell therapy may be effective to improve quality of life in individuals of ID with ASD even in adulthood