We aimed at investigating the impact of coronavirus disease 2019 (COVID-19) on the time required to complete a 1000-m run and vital capacity (VC) among healthy male students at three universities in Wuhan, China, followed for four years covering the prepandemic (2019), early/late pandemic (2020/2021), and post-pandemic (2022) periods. Demographic information including age, body height/weight, and body mass index (BMI) were also collected. After dividing the participants into four groups based on BMI (i.e., underweight: BMI <
18.5
normal: 18.5 ≤ BMI <
25
overweight: 25 ≤ BMI <
30
obese: BMI ≥ 30), the associations of 1000-m run performance with changes in BMI and VC between different groups and within each group in different periods were analyzed. A 4-year follow-up on 10,037 participants demonstrated a progressive deterioration of 1000-m performance (p <
0.001) except the obese group. All participants showed a drop in VC in the post-pandemic period (all p <
0.001) compatible with their impaired 1000-m run performance. The underweight/normal BMI groups also exhibited an annual increase in BMI (all p <
0.001). Impairment in 1000-m performance was most conspicuous during the early pandemic period and as the pandemic subsided. Our findings showed deterioration in physical endurance and VC among university students during the pandemic, highlighting the need for cardiopulmonary exercise reinforcement during a pandemic.