Background: The purpose of this study was to compare physical activity (PA) outcomes in a sample of high school (HS) physical education (PE) lessons from schools that adopted "traditional" versus "modified block" schedule formats. Methods: We used the System for Observing Fitness Instruction Time (SOFIT) to conduct observations of 168 HS PE lessons delivered by 22 PE teachers in 4 schools. T-tests and multilevel models were used to explore variability in moderate PA and vigorous PA. Results: PA outcomes were significantly different between "modified block" and "traditional" schools. Students who attended "traditional" schools engaged in more vigorous PA in PE lessons. "Modified block" lessons lost more scheduled lesson time due to poor transition to and from the locker room. PA outcomes were positively associated with fitness and teacher promotion of PA and negatively associated with lost time, class size, management, and knowledge. Conclusions: Although PE proponents widely advocate for more PE minutes, this study showed that greater time scheduled in PE does not necessarily result in more student accrual of moderate to vigorous physical activity (MVPA) minutes.