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Community-based participatory research is an important strategy to deal with public health challenges. However, the application of community-based participatory research in public health has encountered many challenges. This study was conducted to address academic perspective about the challenges and factors that are influencing on the community-based participatory research in Iran. A qualitative design using a conventional content analysis approach was employed to collect and analyze data. Twenty –one participants were recruited by using purposive sampling. The data were generated through semi-structured interview. In this work, we found that there are different factors that influence the community-based participatory research projects. These factors are categorized into four main categories: "interpersonal relationships", "readiness", "environment-conducive", and "institutional issues". This study yielded valuable results for researchers aiming at implementation of community-based participatory research in Iranian community. Further efforts should be directed towards improving academician capacity and creating systems to support this method of research.