Physical activity (PA) in youth tends to decline with increasing age, while sedentary behaviour including screen time (ST) increases. There are adolescents, however, whose PA and ST do not follow this pattern. The aim of this study is (i) to examine trajectories in PA and ST from grade 7-9 among students in Berlin, and (ii) to investigate the relationship of these trajectories with individual factors and school type. For the present analyses, changes in students' PA and ST across three time points from 7th to 9th grade were assessed via self-report questionnaires. Positive and negative trajectories were defined for both PA (positive: increasing or consistently high, negative: decreasing or consistently low) and ST (vice versa). Multivariable logistic regression analyses were performed to identify possible predictors of PA and ST trajectories. In total, 2122 students were included (50.2% girls, mean age 12.5 (standard deviation 0.7) years). Compared to grade 7, less students of grade 9 fulfilled PA and ST recommendations (PA: 9.4% vs. 13.2%; ST: 19.4% vs. 25.0%). The positive PA trajectory included 44% of all students (63% boys), while the positive ST trajectory included 21% of all students (30% boys). Being a boy was significantly associated with a positive PA trajectory, while being a girl, having a high socioeconomic status, and attending a high school, were significantly associated with a positive ST trajectory. Different PA and ST trajectories among adolescents should be taken into account when implementing prevention programs for this target group.