Background Cerebral Palsy (CP) is a heterogeneous group of conditions that results in permanent motor disability. Recent studies have suggested that cellular transplantation may have functional efficacy in the treatment of CP. We conducted a pilot study of the intrathecal transplantation of autologous bone marrow aspirate (BMAC) concentrate in children with CP to assess the safety of the procedure as well as its potential efficacy in motor and cognitive functions. Materials and methods Twenty-four patients with CP received BMAC and were evaluated 12 months. The treatment procedure involves three intrathecal BMAC applications along with neurorehabilitation. We assessed potential efficacy by using Gross motor functional classification system, Ashworth scale, Learning accomplishment profile-diagnostic scale, brain magnetic resonance imaging and electroencephalogram. Results The study enrolled 24 CP patients with chronological age from 1-12 years but the current developmental age was from 6 -10 months. After BMAC therapy, immediate improvements were noted within first 7 days, decreased muscle tone, and decreased involuntary limb movements, better head control and decreased salivation. After treatment, 83% patients developed relaxation of the extremities. The cognitive function assessment also revealed significant improvement in 40% patients. The average developmental age of the CP patients after the intervention was 22 months in the field of cognition and, 20 months in the field of locomotor skills, 21 months in the field of speech skills. Conclusion Autologous BMAC transplantation seems to be safe and feasible, and can help reduce the degree of impairment of CP patients and, improve the quality of life. The combination of cell therapy and neurorehabilitation can lead to functional restoration that reduces disability in CP.