Objectives This study investigates the construction of a combined system of Western and Oriental medicine at the Korean National Rehabilitation Center. The findings of this study can be used as guidelines for the establishment and management of an Oriental Medicine Department at the Center. Methods The study involved the collection and organization of information regarding combination of Western and Oriental medicine, analysis of the current system, meetings with experts, modifications made on the basis of the meeting results, and assessment of operations to be carried out by the Oriental Medicine Department at the Center. Results This study provided suggestions for the establishment and management of the Oriental Medicine Department at the Center. In addition, it made recommendations for the role that the Oriental Medicine Department can play in the formation of a combined system of Western and Oriental medicine. Thus, the study can facilitate the construction of a combined system of Western and Oriental medicine through the Oriental Medicine Department at the Center in December 2010. Conclusion It is possible to realize patient-centric treatment procedure under the stable and efficient combination of Western and Oriental medicine through the establishment of an Oriental Medicine Department at the Korean National Rehabilitation Center. Such a cooperative system should involve a complete understanding of Western and Oriental medicine and should not be restricted to limited information sharing.