As clinical reasoning is a fundamental competence of physicians for good clinical practices, medical academics have endeavored to teach reasoning skills to undergraduate students. However, our current understanding of student-level clinical reasoning is limited, mainly because of the lack of evaluation tools for this internal cognitive process. This functional magnetic resonance imaging (fMRI) study aimed to examine the clinical reasoning processes of medical students in response to problem-solving questions. We recruited 24 2nd-year medical students who had completed their preclinical curriculum. They answered 40 clinical vignette-based multiple-choice questions during fMRI scanning. We compared the imaging data for 20 problem-solving questions (reasoning task) and 20 recall questions (recall task). Compared to the recall task, the reasoning task resulted in significantly greater activation in nine brain regions, including the dorsolateral prefrontal cortex and inferior parietal cortex, which are known to be associated with executive function and deductive reasoning. During the recall task, significant activation was observed in the brain regions that are related to memory and emotions, including the amygdala and ventromedial prefrontal cortex. Our results support that medical students mainly solve clinical questions with deductive reasoning involving prior knowledge structures and executive functions. The problem-solving questions induced the students to utilize higher cognitive functions compared with the recall questions. Interestingly, the results suggested that the students experienced some emotional distress while they were solving the recall questions. In addition, these results suggest that fMRI is a promising research tool for investigating students' cognitive processes.