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Schools are an important arena to curb the decline in physical activity (PA) in youth. School-based interventions with accelerometer-measured PA are warranted. This study aimed to increase accelerometer-measured PA in adolescents following a 12-month school-based intervention. Two school-classes of 16–18-year-old Swedish students were allocated to intervention group and control group. Accelerometer-measured PA was gathered at baseline, 6-and 12-month follow-up. Mixed-effects linear regression was used to investigate between-group and within-group differences in mean minutes per day (min/day) of moderate to vigorous PA (MVPA), light PA (LPA) and sedentary time (ST). Fifty-seven students participated (intervention group = 31, control group = 26). At 12-month follow-up, the intervention group performed 5.9 (95% CI: −4.3, 16.2) min/day more in MVPA, 1.8 (95% CI: −17.9, 14.2) min/day less in LPA, and 4.1 (95% CI: −27.3, 19.2) min/day less in ST compared to the control group. Within the intervention group, there was no significant change in PA. Within the control group, LPA decreased (95% CI: −19.6, −0.2; p = 0.044) and ST increased (95% CI: 1.8, 30.8; p = 0.028). Although no between-group differences in PA were statistically significant, the within-group changes may suggest a preventive impact on the decline in PA during adolescence.