We examined gender and grade differences in the relationship between students' perceived competence, their enjoyment of physical education (PE), and their PA persistence on the frequency of their physical activity (PA). We also used structural equation modeling to assess the direct, indirect, and total effects of perceived competence and PE enjoyment on PA frequency through the mediator of PA persistence. Participants were 223 middle school students (115 boys, 108 girls) in grades 7 and 8. We found that, regardless of grade level, girls had lower perceived competence and PE enjoyment than boys. Both perceived competence and PE enjoyment had significant direct and positive connections to persistence, but they had no significant indirect effects on PA frequency through the mediator of persistence. These findings highlight the need for physical educators to be aware of gender differences in perceived competence and PE enjoyment, and the important roles these factors have in enhancing students' PA participation.