The goal of this study was to assess the effects of a long-term Cooperative Learning programme in students’ basic psychological needs and their intention to be physically active. A total of 109 students (12-14 years old) enrolled in four different Year 8 classes of Secondary Education agreed to participate. Students were organised into an experimental group (n=56), who experienced a Cooperative Learning intervention programme in Physical Education for five months (five learning units, 40 sessions) and a control group (n=53) who experimented, during the same period, the same learning units under a Direct Instruction approach. A quasi-experimental repeated measure applying a pre-test, post-test comparison group design was followed. The results evidenced statistically significant improvements in the intention to be physically active and the basic psychological needs for autonomy and relatedness only in the group of students who experienced Cooperative Learning.