Very few studies have reported an independent association of the physical activity-related indices with the psychological stress reaction. The present study therefore investigated the association of fitness and screentime as one of the indices of sedentary behavior with the four types of psychological stress reactions and the number of days absent from school for 249 children at a local public school and a metropolitan private school while considering confounding factors. No significant difference was observed in the fitness level of both schools; however, the rate of obesity, the screentime and the level of all psychological stress reactions were significantly worse in the public school. Further, significant differences and trends among the groups classified by fitness level were recognized in the rates of participation in after school activities, feeling of powerlessness and days of absence per year. In addition, the odds ratio of the screentime for depressive and anxiety symptoms was 1.004 (95%CI: 1.000-1.007, p=0.039), while the odds of the fitness level for high feeling of powerlessness and more than five days of absence were 1.582 (95%CI: 1.045-2.396, p=0.030) and 1.434 (95%CI: 1.045-2.396, p=0.015), respectively, after adjusting for the school type, differences in lifestyle and participation in after school activities. In conclusion, the fitness level and the screentime were associated with high psychological stress reactions and the days of absence, independent of the above-mentioned adjusting factors among the children in the present study. Prospective and interventional studies to verify these results are needed.