This research studied the dynamics of Japanese medical students’ emotional intelligence (EI) improved by studying medical history-taking in English during English for Medical Purposes (EMP) classes. The aims of this research are (1) to explore the dynamic structures of medical students’ EI in studying history-taking in English; (2) to examine how the EI improved by studying history-taking in English will influence student’s empathy and test anxiety concerning other medical subjects; and (3) to study self-regulation of students with high academic achivement. Native Japanese speaking undergraduate medical students (N = 67) in Japan participated in this study. After the participants studied patient-centred history-taking through English, which was their second language, for three months, their EI (i.e. empathy, motivation to study EMP, self-awareness, and self-regulation) were assessed by two questionnaires. Explanatory factor analysis across the data showed that Japanese medical students’ EI are explained by three factors: (1) self-awareness of confidence and anxiety during lecture and test (EMP and medical subjects); (2) motivation in EMP and empathy; and (3) self-awareness of confidence in English proficiency. In addition, multiple regression analyses indicated that their improved confidence in English proficiency throughout learning history-taking in English correlated with increasing empathy for patients and decreasing test anxiety in medical education. Moreover, open-ended questionnaire suggested that students with high academic achievements keep higher self-regulation to manage their anxiety and regard anxiety as a vital factor in maintaining motivation for further study in medical education. The study suggests pedagogical implications to develop further curriculum and course materials for undergraduate medical education.