Objectives: Stress can affect learning and memories in students. Prior stress-related studies on students were conducted mainly through surveys. So, we investigated how heart rate variability (HRV)-measured stress 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 exam scores of the end of the school year were also collected. We assessed association between HRV-measured stress and written/skilled exam scores. Results: Written exam scores showed a positive correlation with standard deviation of the N-N intervals (SDNN) (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, with a dominant SNS, and a high stress index had a higher scorer in written exams 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 exam scores were negatively correlated with body mass index (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). Conclusion: This study shows that medical students with higher stress measured by HRV have higher academic achievement, especially in written exam. Further studies are needed to reconfirm the results of this study and to assess the long-term effects of HRV measured stress on medical education.