Impostor syndrome is described as a series of experiences in which an individual is uncertain about their true capability, skills, or achievements. Impostor syndrome may have a negative impact on medical students’ life, especially in the context of their academic performance and leadership virtues. Therefore, we aimed to study the prevalence, factors associated with impostor syndrome, and the association of impostor syndrome and academic performance, as well as leadership virtues. A cross-sectional study among the undergraduate clinical year medical students was carried out in a private medical university in Malaysia. Purposive sampling was used to enrol students for this study, the data were collected by the distribution of an online questionnaire and a total of 90 participants responded. We calculated the independent t-test using Epi info software. Among the students, 47.8% of students were suffering from impostor syndrome. Factors such as gender, ethnicity, nationality, intention to pursue fellowship, and parents’ occupation had an insignificant association with impostor syndrome. There is a significant association between impostor syndrome and subjective academic achievement and the students who did not have the syndrome perceived they performed well academically. The students without impostor syndrome had better leadership skills than the students who had impostor syndrome, however, it was not significant. In summary, impostor syndrome is quite common among students who are pursuing the medical course, thus more attention should be given to this issue. We recommend the education institution to introduce more motivational programmes to increase the confidence level of the students.