Physical activity contributes to children’s physical and mental well-being. Research suggests that active free play helps to maintain and increase physical activity in children and also contributes to social and emotional well-being. To date, these studies have focused on Western countries. Thus, this study was conducted to gain insights into the factors of perceptions of fun, barriers, and facilitators affecting active free play from the perspective of Japanese children using focus group interviews. In Japan, 12 focus groups were conducted with 60 children aged 9–11 years. Children’s perceptions of fun in active free play were categorized into socializing, achievement, emotions, and freedom. Additionally, active boys' groups were interested in free play and adventure play; girls' groups were interested in free play with less physical movement and challenges; inactive boys' groups were interested in relaxing and competitive play with bodily contact. However, children mentioned that busy schedules, weather, and health-related factors acted as main barriers. Lastly, children noted facilitators include setting schedules, having access to equipment and playgrounds, and holding special events. The findings provide insights into active free play-related factors for active and inactive Japanese children and also clarify the differences between Japanese and Western children. Such findings will contribute to designing interventions to increase active free play.