Game-based learning environments typically elicit a variety of emotions; however, the influence of emotions on game-based learning is basically underemphasized. This study sought to investigate how emotions are related to science learning in a gaming context. "Humunology," an educational game for learning about the human immune system, was used, and 112 seventh graders aged 12-13 years old took part. The results indicated that learning through playing "Humunology" was effective and that the long-term effect of this approach on learning retention was promising in comparison to traditional web-based instruction. A cluster analysis by the K-means algorithm categorized the students who learned through playing "Humunology" into two core groups. Students in cluster 1 experienced substantial levels of both positive and negative emotions while learning through playing "Humunology," whereas the students in cluster 2 experienced primarily positive emotions. Although students who experienced primarily positive emotions had better learning outcomes right after playing "Humunology," the learning effect declined as time passed, to the extent that they performed the same as those who experienced both positive and negative emotions in terms of long-term learning retention. The significant findings of the study and their interpretations are discussed, and limitations and suggestions for future work are provided.