Strenuous exercise induces upper respiratory tract infection (URTI), whereas moderate exercise prevents URTI. This study aimed to assess the incidence of URTI and the association between URTI episodes and exercise duration in Japanese collegiate athletes. A cross-sectional survey was conducted with 1,740 participants; 1,235 responses were eligible for analysis. Participants were classified into three groups: control group (weekly total exercise duration <60 min, n=405), exercise group (weekly total exercise duration >60 min, n=193), and athlete group (joined a sports club and weekly exercise frequency >5 days, n=637). We requested the following information from participants: basic characteristics, incidence of URTI symptoms (fever, runny or plugged nose, sore throat, and cough) or influenza for each month over the past year, day of the week exercise is typically performed, and duration of exercise per week. The incidence of URTI episodes per year was significantly lower in the athlete group (2.0 ± 2.4 episodes) compared to the control group (2.6 ± 2.4 episodes, p<0.001). The incidence of URTI episodes did not significantly differ between the control group and exercise group (2.9 ± 2.9 episodes, p=0.607). Although the frequency of URTI episodes and exercise duration were not significantly associated among male athletes (p=0.209), they were positively associated in female athletes (p=0.027). These results indicate that Japanese collegiate athletes experience fewer URTI episodes than non-athletes, but athletes who exercise for long durations may frequently experience URTI, particularly female athletes.