Background: Clinical assessment in medicine is a pillar of education, which should measure the competence and practical abilities of medical students. The viewpoint of students as one of the most important stakeholders in clinical assessment could guide planners in problem-solving and proper corrective actions. Objectives: The present study aimed to investigate the influential factors in the performance of medical students in the clinical competency exam. Methods: This qualitative study was conducted using the directed content analysis approach during 2018 - 2019. The sample population included 10 medical students of internship at Isfahan University of Medical Sciences in Isfahan, Iran. The participants were selected via purposive sampling. Data were collected via semi-structured interviews. Data analysis was performed in the MAXQDA 10 software. Results: The students mentioned several influential factors in their performance on the competency exam. Their viewpoints were divided into seven categories, including content and resources, pre-exam requirements, time, cases (scenarios), stations, examiners, and the role of the clinical training course. Conclusions: Similar to other clinical exams, the clinical competency exam has some drawbacks despite its positive aspects, which may affect the performance of students. Several factors could influence the performance of students in this exam, and the contribution of these factors and their impact on the performance of students vary. Therefore, special attention should be paid to these factors to help officials and policymakers in future planning and improving the quality of these exams.