Objective: To evaluate the clinical effect of Traditional Chinese Spinal Orthopedic Manipulation (TCSOM) in treating Functional Abdominal Pain Syndrome (FAPS) in comparison with Pinaverium Bromide (Dicetel, PBD), and to assess a possible cause for FAPS. Methods: 60 cases of FAPS patients were randomly assigned to the TCSOM group and PBD group according to the random number table method. The TCSOM group was treated with thumb pressing manipulation, every other day in the first week, and once every three days in the second week, for 5 times treatments. Patients in the PBD group were instructed to take 50mg 3 times a day, consistently for 2 weeks. The symptoms of pre-treatment and post-treatment were assessed on a visual analog scale (VAS) pain score. A symptom improvement rating (SIR) was implemented in order to evaluate the effects of the treatments, and to statistically compare the two groups. Results: The symptoms of 21 patients of the TCSOM group were resolved soon after the first spinal manipulation treatment and 4 cases were significantly improved. The VAS pain scores in the TCSOM group were significantly lower than those in the PBD group after 2 weeks treatment. According to the SIR based on VAS, the TCSOM research group included 20 cases with excellent results, 8 cases with good, and 2 cases with poor. There were no side effects in the TCSOM group after treatment. Based on VAS, the PBD research group reported 6 cases with excellent results, 8 cases with good and 16 cases with poor. All cases were statistically analyzed, revealing a significant difference (P<0.001) between the two groups. Conclusion: TCSOM group performed much better than PBD group for relief of the symptoms of FAPS. Thumb pressing manipulation on the thoracic and/or lumbar region can correct the displacement of inter-vertebral discs and/or vertebra, resolving the stimuli caused by pressure exerting on the nerves and vessels around the spine.