Background: Few youth engage in sufficient daily moderate-to-vigorous physical activity (MVPA), and the likelihood of meeting guidelines declines through secondary school. Physical education (PE) can afford youth with opportunities for MVPA. Therefore, the purpose of this study was to investigate the impact of changes in PE enrollment on MVPA and MVPA guideline adherence in Ontario and Alberta secondary students. Methods: Linked survey data was used from 1514 students who participated in year 3 (2014/2015 baseline) and year 6 (2017/2018 follow-up) of the COMPASS Study. Regression models tested whether changes in PE enrollment predicted changes in self-reported MVPA (minutes) and MVPA guideline adherence from grade 9 (baseline) to grade 12 (follow-up), controlling for sports participation and sociodemographic variables. Results: Students who remained enrolled in PE in grade 12 reported a daily average of 30 minutes more MVPA. Among students meeting MVPA guidelines and enrolled in PE in grade 9, students not taking PE in the current term in grade 12 were less likely to continue to meet guidelines than students currently enrolled in PE (adjusted odds ratio 0.53; 95% confidence interval: 0.36, 0.78; p < .0013). Conclusions: Findings from this study could inform the future implementation of a mandatory PE credit for upper year secondary students.