Background: Our study aimed to examine the effects of COVID-19 on the physical fitness and academic performance of Chinese college students. Participants: The sample included physical fitness test data from 9,712 undergraduate students and academic performance data from 12,000 undergraduate students at a top university in China. Methods: Physical fitness was measured and evaluated according to the Chinese National Student Physical Fitness Standard. Data were analyzed using two-sample t-tests and Pearson product-moment correlations. Results: Total physical fitness test scores of college students decreased after the outbreak, but their mean body mass index (BMI) remained at normal levels. The mean academic performance of college students unexpectedly improved during the online learning period. The positive correlation between physical test scores and academic performance was significantly higher during COVID-19 than that before the outbreak. Conclusions: Chinese college students with high physical fitness during COVID-19 were more likely to achieve good academic performance.