Introduction: A new training strategy in many medical universities around the world, which has been considered by educational planners, is interprofessional education (IPE). The main aim is designing and implementing IPE, reinforcing teamwork and collaboration among the health team members. This study has been done aiming to explore effective factors in the designing and implementing IPE in health system of Iran from the perspective of faculty members. Methods: This qualitative study used content thematic analysis methodology. A purposive sampling was used and continued until the data were saturated. The participants were six faculty members with more than 5 years of teaching experience or educational activities in Educational Development Center (EDC) or Educational Development Office (EDO). Results: The four main themes emerged from the interviews were classified as follows: the structure of the educational system, economic issues, cultural atmosphere, and social conditions. They were all associated with some positive factors such as curriculum changes and reforms, design and implementation of the interprofessional education in various forms and some negative factors such as lack of physical structure appropriate for the IPE in the universities, promotion of culture of individualism and uni-professionalism, etc. Conclusion: The results of this study showed that in our country, the effect of educational, cultural, social and economic barriers on the development and implementation of IPE, and also, unfamiliarity of educational system with the various aspects of IPE, has made the implementing of these programs in the curricula of different professions of health sciences difficult.