This study investigated the effects of a pedagogical agent that cued relevant information in a story-based instructional animation on the cardiovascular system. Based on cognitive load theory, it was expected that the experimental condition with the pedagogical agent would facilitate students to distinguish between relevant and irrelevant information, and therefore lead to higher learning outcomes and lower cognitive load than the control condition without a pedagogical agent. Based on 133 seventh-grade students as participants, the results confirmed the hypotheses, indicating that the pedagogical agent had a more positive effect on learning outcomes and resulted in a more favorable relationship between learning outcomes and cognitive load. The results are discussed in terms of theoretical and practical implications for designing instructional animation.