Objective: The present study aimed to examine the relationship between physical fitness and academic performance, after controlling for potential confounds. Participants: The sample comprised 2,324 college students representing three Chinese universities. Methods: Physical fitness was measured using the Chinese National Student Physical Fitness Standard; academic performance (i.e., Grade Point Average) and lifestyle behaviors were assessed using questionnaires. Academic performance and overall physical fitness were used to divide participants into three categories: low, moderate, and high. Results: Several physical fitness indicators systematically differed across the three academic performance categories. Additionally, overall physical fitness was positively associated with academic performance, even after controlling for the effects of lifestyle behaviors; those who belonged to the high overall physical fitness group had lower odds ratios of low academic performance than those belonging to the low overall physical fitness group. Conclusions: Poor academic performance was related to low overall physical fitness. The probability of having poor academic performance was significantly lower among students with high physical fitness than those with low physical fitness.