The goal of the study was to contrast the effects that a Cooperative Learning implementation in Physical Education can produce in two different Educational stages: Primary and Secondary Education. A total of 179 students agreed to participate: 96 (44 boys, 52 girls) were enrolled in four Year 7 Primary Education groups (11.37 ± 0.89 years) and 83 students (38 boys, 45 girls) were enrolled in three Year 11 Secondary Education groups (15.42 ± 1.12 years). Convenience sampling was used. All groups experienced three consecutive learning units (23 sessions). At post-test, motivation increased significantly in the two groups (p = 0.031, p = 0.029), while social interaction only in the Secondary Education group (p = 0.024), and a significant difference between groups was also obtained in the post-test (p = 0.034). All effect sizes exceed the value of 0.87, which is considered large. Qualitative data showed that the teacher highlighted the importance of cooperation in Physical Education in order to promote respect for others and joint thinking in Primary Education.