Objective To investigate the physical fitness level of first-year to fourth-year undergraduate medical students at a medical university in Beijing, and explore its influencing factors. Methods Physical fitness tests were conducted on students from September to November 2023, according to the "National Student Physical Health Standards (Revised in 2014)". Failing the test was used as the outcome variable. Univariate and multivariate binary logistic regression analysis were performed to explore the relevant influencing factors. Results Among the 3 975 medical students who participated in the test, 3 693(92.91%) passed, while 282 (7.09%) failed. Univariate logistic regression results showed that junior year (OR=1.469), "5+3" education program (OR=1.113), and non-medical degree (OR=1.156) were risk factors for poor physical health. Being female (OR=0.235), older in age (OR=0.733), non-Han ethnicity (OR=0.799), sophomore year (OR=0.409), and five-year program (OR=0.854) were protective factors. Multivariate analysis indicated that being female (OR=0.341) and sophomore year (OR=0.403) were protective factors. Junior (OR=1.579) or senior year (OR=1.219), and higher body mass index (BMI) (OR=1.356) were risk factors for failing the physical fitness test. Conclusion The university should strengthen the campus sports culture, provide targeted education for key student groups, plan sports projects and activities, promote work-leisure balance among medical students, and increase their awareness and enthusiasm for physical exercise.