The effect of screen time during secondary school on percent body fat was examined in a cohort of 744 Canadian adolescents aged 12-13 years at baseline. Participants completed self-reported questionnaires on television viewing and computer use in 19 survey cycles over 57 months from 1999 to 2005. Triceps skinfold thickness and subscapular skinfold thickness were measured in survey cycles 1 and 19. Four screen-time trajectory groups identified in growth mixture modeling included steady-low screen time (73% of the sample), steady-high (10%), increasers (9%), and decreasers (8%). The effect of screen-time trajectory on percent body fat at survey cycle 19 was modeled in boys and girls separately by using linear regression, adjusting for baseline percent body fat and physical activity. Relative to that of steady-low screen-time trajectory group boys, percent body fat was 2.9 (95% confidence interval: 0.7, 5.0) and 2.4 (95% confidence interval: 0.5, 4.2) percentage units higher on average among "increasers" and "steady-high" trajectory group boys, respectively. There was no evidence that screen time has an effect on percent body fat in girls overall, although physical activity modified the association between screen time and percent body fat in both sexes. Efforts to prevent obesity in youth should emphasize reducing screen time.