Purpose: Low back pain is a significant problem for school-aged athletes. Although some risk factors relating to sports activities have been reported, the effect of lifestyles on low back pain in school-aged athletes is not clear. The purpose of this study was to elucidate the association between lifestyles, such as wake-up time, bedtime, sleeping time, and TV-viewing or video-game-playing time per day and low back pain of school-aged athletes. Methods: A cross-sectional study was conducted with school-aged athletes (aged 6–15 years, n = 6441) using a self-reported questionnaire and multivariate logistic regression models were used for analyses. Variables considered in the models were gender, age, body mass index, team levels, number of days in practice per week, number of hours in practice per day, and lifestyles. Results: The frequency of low back pain was 5.0% (n = 322). Late bedtime, short sleeping time, and long video-game-playing time per day were significantly associated with low back pain. There was no significant association between low back pain and wake-up time or TV-viewing time per day. Conclusion: Unhealthy life-style choices, such as late bedtimes, short sleeping time, and longtime video-game playing, were associated with low back pain in school-aged athletes.