The purpose of this study was to examine the association of screen viewing time (SVT) and study time (ST) with physical fitness among second-year high school students. This cross-sectional study was carried out including 678 (boys: n = 322) students enrolled from 2011 to 2013. Physical fitness measurements included muscular fitness, explosive power and endurance performance. Muscular fitness and explosive power were evaluated by grip strength and standing broad jump test, respectively. Endurance performance was evaluated by endurance running speed of 1500 meters (in boys) or 1000 meters (in girls) running. SVT, ST and other lifestyle behaviors were obtained by a self-reported questionnaire. Analysis of covariance was used to examine the association of SVT and ST with grip strength, standing broad jump distance and endurance running speed. After adjustment for potential confounders, longer SVT was associated with poorer endurance running speed in both boys and girls, (p for trend < 0.01). Longer SVT was also associated with lower standing broad jump distance in boys (p for trend = 0.007) and grip strength in girls (p for trend = 0.005). In boys, longer ST was also associated with lower grip strength after adjustment for potential confounders (p for trend = 0.007). In conclusion, these results suggest that differences between SVT and ST may have different effects on physical fitness data 3-year after the earthquake disaster. Further studies are necessary to confirm the findings of this study.