Children's screen time may affect their growth and development. However, different aspects of children and their parents that affect children's screen time has not been investigated in the Japanese context. This study aimed to explore the relationship between relevant factors affecting children's screen time based on their sleep, difficulties, and parental control, among Japanese elementary and junior high school students. A cross-sectional survey was conducted among parents in Japan. Data on screen time duration, parent-child background, strengths and difficulties, sleep variables, and parental control types were collected from 225 households. Path analysis revealed that high Strengths and Difficulties Questionnaire (SDQ) scores (β = 0.167, p = 0.007), sleep duration (β = -0.282, p < 0.001), and parental control (β = -0.205, p < 0.001) were significantly related to children's screen time. Additionally, late parental bedtime negatively correlated with children's sleep duration (β = -0.326, p < 0.001). The findings suggest that children's difficulties, sleep duration, and parental control are associated with children's screen time. This study, together with previous research, provides comprehensive insights to design interventions to decrease screen time in children in the Japanese context.