Jigsaw is an attractive cooperative method for implementing physical education (PE). However, Jigsaw is a demanding method for students and teachers and requires time. Thus, the time required for the implementation of Jigsaw is important with respect to its potential effects on students. Previous findings regarding the effects of Jigsaw on students’ learning in the educational field have been inconsistent, and the consequences of the method on students’ engagement remain understudied. In PE, differences between boys and girls are well known, notably with respect to their engagement in physical activity (PA). The purpose of this study was to investigate the effect of Jigsaw on moderate to vigorous PA (MVPA) in PE classes in light of student sex and habituation (through one sequence and during several sequences). Overall, 254 secondary school students participated in the study. MVPA was measured during the third and sixth lessons of three different PE sequences during a school year. Linear mixed model analyses were performed while controlling for the type of activity taught in PE and the class. The results showed that the Jigsaw condition was associated with smaller sex differences than the control condition. Moreover, differences between the two conditions decreased with habituation through one sequence in favor of Jigsaw but not through three sequences. The results suggest that Jigsaw could be used to reduce inequalities between girls and boys in PE and that long sequences based on a specific activity seem to be preferable to successive sequences involving various activities.