Introduction: Pain is a major symptom in many medical conditions and is significantly associated with alteration of the quality of life and individual as well as overall performance. Pain is one of the main problems in patient with spinal cord injury. Spinal cord injury is one of the causes of chronic pain that occurs due to temporary or permanent changes in spinal cord function. Traffic accidents, war injuries and sports injuries are the major reasons. Clinical decision support system separates intelligently expert's information and knowledge for physician, health professionals, and patients as well as other individuals and represents the knowledge in right time to provide more efficient treatment and health care. Automated health information systems are gathering data and information to support the integration of managerial decision-making processes. Conclusion: Paper-based systems are not suitable for repetitive clinical evaluations of patients with spinal cord injury. Design and implementation of automated systems for gathering information in pain management and physician assistant to medical decision making for pain diagnosis in patients with spinal cord injury are very effective. This system may use different artificial intelligence techniques, including Bayesian networks, artificial neural network, decision trees, and fuzzy logic.