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Purpose: Academic failure tolerance (AFT) is one of the important psychological concepts in education, but its applications in medical education are rare. Thus, the purpose of this study was to investigate the effect of academic failure tolerance on academic achievement fluctuation among medical school students using a longitudinal research design. Methods: The subjects were 43 medical students who responded to the AFT test. This study analyzed the longitudinal data of achievement scores up to the 2nd academic year (2012–2013) among students who were divided into academic achievement improvement and decline groups. Results: Comparing the improvement and decline groups’ mean academic achievement fluctuation scores demonstrated that behavior and preferred task difficulty showed high scores whereas feeling scores were lower in the improvement group (p<0.05). Conclusion: In the improvement group, despite the higher negative feeling scores during academic failure, the students favored the more difficult subjects and were more assiduous in their studies. This will form an important basis for enhancing academic achievement among medical students.