OBJECTIVES: Stress can affect learning and memory in students. Previous studies on stress in students were conducted mainly through surveys. We investigated how heart rate variability (HRV)-measured stress is related to academic achievement in medical students during clerkship. SUBJECTS AND METHODS: A cross-sectional study was conducted. HRV measurements were performed in 97 third-year medical students during their family medicine clerkship course. Data on written and skilled examination scores of the end of the school year were also collected. We assessed the association between HRV-measured stress and written/skilled examination scores. RESULTS: Written examination scores showed a positive correlation with standard deviation of the normal-to-normal intervals (SDNNs) (r = 0.245, p = -0.016), sympathetic nervous system/parasympathetic nervous system (SNS/PNS) balance (r = 0.218, p = 0.033), and stress index (r = 0.381, p = 0.004). Students with an unhealthy SDNN, a dominant SNS, and a high stress index had higher scores in written examinations than students with a healthy SDNN, a balanced SNS/PNS, and a normal stress index, respectively (p = 0.004, 0.018, and 0.012, respectively). Moreover, skilled examination scores were negatively correlated with BMI (r = -0.249, p = 0.014) and were higher in female students (r = 0.240, p = 0.018). Students with an abnormal autonomic balance diagram (ABD) had a higher score than students with a normal ABD (p = 0.03). CONCLUSIONS: This study shows that medical students with higher stress measured by HRV have higher academic achievement, especially in written examinations. Further studies are needed to confirm the results of this study and to assess the long-term effects of HRV-measured stress on medical students.