This study aimed to (1) evaluate the effects of an empathy education program, and (2) explore functional magnetic resonance imaging (fMRI) as a potential empathy assessment tool. An empathy enhancement program for premedical students was developed. The Korean version of the Jefferson Scale of Empathy-Student version (JSE-S) and Interpersonal Reactivity Index (K-IRI) were used to measure self-assessed changes in empathy. Clinical vignettes demonstrating empathy tasks were presented to participants undergoing fMRI, to assess regional changes in the brain. Self-reported empathy scores and brain activity signals using fMRI from before and after the program were compared. The JSE-S total and perspective taking scores significantly increased after the program. Data from the fMRI revealed noticeable differences in cognitive regions associated with empathy, namely the right superior medial frontal gyrus and left precentral gyrus. This study results support the prior evidence of positive impact of empathy education. In addition, the authors suggest that brain fMRI might be used in measuring the effectiveness of empathy education.