Several authors have underlined the negative consequences of the COVID-19 pandemic on mental health in several populations, including medical students, such as increases in anxiety, depression and burnout symptoms. Furthermore, previous studies showed that anxiety and depressive symptoms are positively associated with affective empathy and negatively associated with cognitive empathy. Given the adverse pandemic effects highlighted by several authors, the present study sought to determine whether medical students' empathy has been potentially impacted, with higher affective empathy and lower cognitive empathy score in the pandemic cohort compared to pre-pandemic cohorts. Medical students (n = 395) were recruited during the COVID-19 pandemic and completed the "Interpersonal Reactivity Index" (IRI) and the "Basic Empathy Scale" (BES). This cohort was then compared with two pre-pandemic cohorts (one used the BES [n = 1168], and the other used the IRI [n = 342]). Similar results were found on both scales: the pandemic cohort displayed significantly higher scores in affective empathy and personal distress (affective empathy domain) and, surprisingly, significant higher scores in cognitive empathy, fantasy, and perspective-taking (cognitive empathy domains). As stressed by previous studies, we posited that the higher scores in affective empathy, personal distress, and fantasy might indicate emotional difficulties. The paper concludes with the identification of empathy components that should be promoted in the curriculum of medical students.