Although research on COVID-19 is prevalent, risk factors for contracting COVID-19 and lifestyle changes in athletes during the COVID-19 pandemic have not been thoroughly investigated. This study included 254 female collegiate athletes and 107 female non-athletes from Japan, who completed an anonymous survey comprising questions about COVID-19, personal background and lifestyle changes during the pandemic. A total of 6.30% athletes and 6.54% non-athletes had tested positive for COVID-19. The majority reported no change in menstrual cycle (80.31% and 78.50% for athletes and non-athletes, respectively). Wake-up time and bedtime were delayed in some athletes (42.13% and 39.25%, respectively) and non-athletes (46.73% and 31.30%, respectively) during the pandemic. Body mass index (BMI) was significantly higher in COVID-19 (+) athletes than in their COVID-19 (−) counterparts (22.78 ± 3.40 and 21.26 ± 2.06, respectively, p < 0.01) and logistic regression analysis revealed that younger students and those with higher BMI had an increased risk of contracting COVID-19. The proportion of vaccinated students was significantly higher in athletes than in non-athletes (p < 0.01). Whether the student was an athlete or not was not a related factor in contracting COVID-19. Extra attention should be focused on athletes experiencing weight gain or staying up late and experiencing lower quality sleep.