This study aimed to determine whether adolescents’ leisure screen time differed during the coronavirus disease 2019 (COVID-19) pandemic compared to before the pandemic, and to identify factors that affect leisure screen time among Japanese high school students. The Health Behavior in School Children questionnaire was used to investigate differences in eating habits and physical and mental health. The results showed that the leisure screen time of Japanese high school students was 2.6 h (SD = 1.4) before the pandemic, and 3.2 h (SD = 1.5) during the pandemic. The factors that increased leisure screen time were found to differ between boys and girls. No significant deterioration in physical and mental health was observed. The impact of the pandemic on eating habits differed in boys and girls. Boys reported “not feeling great about life” as a factor that increased leisure screen time during the pandemic, suggesting that negative emotions influenced the increase in leisure screen time. The pandemic had a significant impact on girls’ leisure screen time. Longer screen time should be carefully monitored because it can lead to sleep disturbances, worsening of mental health, and obesity. Compared with before the pandemic, the health status of boys and girls changed little. Eating habits tended to improve for both boys and girls.