Introduction: Faculty members’ evaluation is an important factor for promotion, tenure, payment of rewards or incentives, accountability and continuation of developing faculty at medical university. Studies showed that having a fair and meaningful faculty evaluation system has an impact on the performances of all faculty members. The present study aimed at investigating the challenges of faculty about faculty members’ evaluation systems. Methods: In this qualitative content analysis study, participants were 10 faculty members from the Tehran University of Medical Sciences. The participants were selected through purposeful sampling. The data which were collected through semi-structured interviews were used for establishing the codes, subcategories, and main categories. The collected data were analyzed by constant comparative analysis being recommended by Corbin and Strauss 2015. Results: The challenges of faculty evaluation system were explored in four main categories: “providing feedback for the faculty”, “objective evaluation", "evaluation based on student perspective”, and “faculty members’ performance analysis". Discussion: This study founded the faculty members who preferred to receive feedback, qualitative evaluation, the need for multiple sources of information gathering, greater transparency, increased trust, and accreditation of the evaluation process. It is recommended to explore the process of faculty evaluation in Iran.