Lower levels of physical activity are associated with childhood obesity. School physical education (PE) policies have been identified as critical to improve child and adolescent physical activity levels but there has been little evaluation of such policies. In the province of Manitoba, Canada, the government implemented a mandatory PE policy in secondary schools designed to increase the daily physical activity levels of adolescents. The objective of this study was to examine the longitudinal changes in and the factors associated with the physical activity trajectories of adolescents in Manitoba during their tenure as secondary school students in the context of this school PE policy. The results found, despite the PE policy, a grade-related decline in the physical activity trajectories of adolescents; however, the decline in physical activity was attenuated among adolescents with low and moderate baseline physical activity compared to adolescents with high baseline physical activity and among adolescents who attended schools in neighbourhoods of low compared to high socioeconomic status. There are several possible explanations for these findings, including the influence of the PE policy on the PA patterns of adolescent subpopulations that tend to be at higher risk for inactivity in both childhood and adult life.