Purpose: To understand how a season of sport education (SE) and a hybrid SE and cooperative learning season impacted on elementary school students’ physical activity levels and motivation and to examine possible differences according to gender. Method: A total of 97 fourth- to fifth-grade students in four intact classes participated in a 14-lesson handball season. Results: Students in SE had higher levels of moderate-to-vigorous physical activity levels than the hybrid season. When sorted by gender, boys were significantly more active than girls in both interventions. However, students in the hybrid season reported higher levels of motivation than participants in the SE season, especially for intrinsic motivation. Conclusion: The hybridization of models positively affected students’ motivation in PE, while the reverse is true of SE with regard to physical activity levels.