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This cross-sectional study investigated regional differences in outdoor playtime and screen time among preschool-age children in Japan, and their associations with environmental factors, in order to identify the modifiable determinants of the differences between urban and rural areas. Data were obtained from the “Eat, be active, and sleep well” study. Children from three (n = 872) and five (n = 744) kindergartens in urban and rural regions of Japan, respectively, who completed a questionnaire survey, were sampled. Finally, data from 1128 participants (age: 3–5 years) were analyzed. To assess the environmental factors, the International Physical Activity Questionnaire was used for neighborhood environments; the Global Physical Activity Questionnaire was used for physical home environments; and a three-item questionnaire was used for sociocultural environments. Outdoor activity was significantly associated with items related to the mother’s sedentary time and the number of siblings/friends in both urban and rural regions. Screen time was associated with the mother’s screen time, television in the room, and esthetic qualities, which were consistent between urban and rural regions, while screen time was associated with night-time crime rates and traffic in the urban region. Our study further bolsters evidence suggesting that outdoor playtime and screen time are strongly associated with various environmental factors among Japanese preschool-age children.