Purpose: The objective of the study was to evaluate the relationships among the achievement emotions experienced during physical education classes, the intention to be physically active, and academic achievement. Methods: The sample consisted of 764 Spanish secondary education students (348 boys and 416 girls). Results: Pride, enjoyment, and hopelessness were the main emotions to explain the intention to be physically active, whereas enjoyment and boredom were the most important emotions to explain academic achievement. Given that boys had a better emotional experience than girls, the effect of gender in the prediction was studied. It highlights the significant moderating effect of gender for enjoyment and pride in the intention to be physically active. Discussion/Conclusion: These results show the need to apply strategies focused on each emotion, taking into account the students’ gender, for those that help to improve their emotional experience during physical education classes.