This research aimed to measure in-class physical activity levels during physical education in grades seven to nine, and to determine the influence of gender and lesson content on such activity levels. Data was collected from 96 lessons across 14 secondary schools. Heart rate data consisted of 821 valid measurements. The mean heart rate across the data set was 135 beats per minute and students engaged in moderate-to-vigorous physical activity 41% of lesson time. Students were most active during game lessons and there was an evident gender difference, with boys being more active. However, when the impact of lesson content and gender on physical activity were tested simultaneously by multi-level logistic regression, the impact of gender was no longer significant. The findings indicate that the gender difference in the activity levels was rooted in having different lessons content for gender groups with boys having games more often than girls do.