Based on the control-value theory, this study examined connections between the perceived in-class degree of cooperation and academic performance mediated through the students' negative and positive emotions in physical education. Students (N = 620, 55.5% girls; M (age) = 13.01, SD = 2.10) reported on their perceptions of the degree of cooperation and the negative (shame, hopelessness, anxiety, boredom) and positive (confidence, pride, enjoyment, calmness) emotions in physical education classes. Academic performance was obtained from their school's administrators. Results from the multiple lineal regression analyses, considering the in-class degree of cooperation and the negative and positive emotions as predictor variables, showed a significantly positive link between the in-class degree of cooperation and the dependent variable academic performance, and between positive emotions and academic performance. These findings elucidate the impact of cooperative learning contexts and emotions on academic performance. Educational implications and future research are discussed.