Background: This retrospective observational study analyzed the therapeutic efficacy of autologous bone marrow mononuclear cells (BMMNCs) in a large cohort of patients with autism spectrum disorder (ASD). Methods: Overall, 1,011 patients with ASD who received intrathecal administration of autologous BMMNCs were included. Changes in symptoms and outcome measures—the Indian Scale of Autism Assessment (ISAA) and Childhood Autism Rating Scale (CARS)— were recorded. Brain positron emission tomography computed tomography (PET/CT) was used to objectively assess changes in brain metabolism. Results: At a mean follow-up of 19.3 months, 90.6% of patients showed improvement after cell therapy. Symptomatic improvements were observed in attention and concentration, command following, eye contact, sitting tolerance, social interaction, hyperactivity, communication, speech, stereotypical behavior, aggressiveness, and self-injurious behavior. Patients who received multiple doses of cell therapy demonstrated better outcomes, and improvements were seen across all age groups and regardless of disease severity. Changes in ISAA and CARS scores were statistically significant (P<0.05).Comparative PET/CT scans of 401 patients revealed improved metabolism in the amygdala, hippocampus, parahippocampal gyrus, caudate nucleus, cerebellum, mesial temporal lobe, thalamus, and superior and middle temporal poles, which corresponded to symptomatic improvements. No major adverse events were reported. Nine of the 1,011 patients experienced seizures, four of whom had a prior history. These events were managed with medication, with improvements still observed in the nine patients. Conclusions Intrathecal transplantation of autologous BMMNCs, combined with neurorehabilitation, yields positive outcomes for patients with ASD. This approach helps reduce the degree of impairment and improves quality of life.