Purpose The purpose of this study is to determine whether there is any change in the empathy scores of third-year medical graduate students after they have taken a clerkship and have begun gaining more opportunities to meet patients through the clerkship. Methods The participants were 109 third-year students in 2014 and 110 fourth-year students in 2015 at Kyungpook National University, School of Medicine. The author measured empathy using a modified and expanded version of the Korean version of the Jefferson Scale of Empathy of Physician Empathy-Student version and used the Holland-III aptitude test-S to assess vocational aptitude. Results As a results, male students in their third year exhibited higher scores, but there was no significant difference in the fourth year. The empathy score increased slightly when third-year students became fourth-year students, but the difference was not statistically significant. There was no statistically significant change in the scores of both male and female students between the 2 years. The results of the vocational aptitude test showed that students who preferred person-oriented specialties had higher empathy scores when they entered their fourth academic year compared to objectively-oriented students. Conclusion In this study, male students showed higher empathy scores than female students, an atypical finding that was inconsistent with the results of previous studies. However, the distribution of scores among male students was wider than that of female students, a finding consistent with previous studies. As such, individual differences need to be considered when developing curriculum in order to improve the empathy of medical students.