The current focus of meeting the physical activity guidelines for children and young people include preventing conditions such as high blood cholesterol, high blood pressure, metabolic syndrome, obesity, low bone density, depression, and injuries. However, the relationship between sleep habits and meeting physical activity guidelines is still unclear. This study aimed to assess this relationship among fifth- to eighth-grade (ages 10–14) Japanese children. This cross-sectional study included 3,123 children (boys: 1,558, girls: 1,565, mean age: 12.5 ± 1.2 years). Questionnaires were used to assess parameters such as moderate-to-vigorous physical activity per day, school and weekend night sleep durations, social jetlag, daytime sleepiness, napping, screen time, and breakfast intake. Participants were divided into an achievement and a non-achievement group depending on their physical activity guideline achievement status (i.e., whether they met the children’s physical activity guideline of 60 min or more of moderate-to-vigorous physical activity per day). Then, to determine the sleep habits in relation to the children’s achievement of guideline-recommended physical activity levels, multivariate logistic regression analyses were conducted. In fifth- and sixth-grade (ages 10–12) boys, an inverse association was observed between physical activity guideline achievement and daytime sleepiness. In seventh- and eighth-grade (ages 12–14) boys, physical activity guideline achievement was inversely associated with social jetlag and skipping breakfast. Additionally, in seventh- and eighth-grade girls, physical activity guideline achievement was inversely associated with inappropriate sleep duration on weekends and screen time. These results suggest that meeting the physical activity guideline is related to favorable sleep habits in Japanese children. However, their relevance may differ by school type and gender.