Introduction: Pain assessment in non-verbal patients during medical interventions can be challenging due to communication problems. Therefore, it is necessary to use new pain measurement tools for these patients. Objective: The objective of the study was to assess the incidence of pain in patients with cerebral palsy (CP) and autism spectrum disorder (ASD) who undergo bone marrow aspiration (BMA) and lumbar puncture (LP) for cell therapy. Methods: The "Non-Communicating Children's Pain Checklist-Revised" checklist was used to observe the behavior of 15 patients diagnosed with CP and ASD before and after cell therapy. The evaluation was carried out simultaneously by a caregiver and by the staff of the medical team on three occasions. Scores ≥ 7 were considered as the presence of moderate or severe pain. Results: Regarding the scores obtained in the second survey (30 min after the BMA and LP), the caregivers reported values of < 7 points in 10 patients (66.7%). At the same time, in the evaluation performed by caregivers 24 h after the procedure, scores of < 7 points were reported in eight (53.3%). The items with the highest scores in the surveys were verbal and facial expressions, social attitudes, and activities. Conclusions: The procedures carried out in cell therapy were safe and well-tolerated by this group of patients, with an incidence of pain in only 33.3%, which can be considered a therapeutic alternative to improve their current condition without compromising their integrity or quality of life.