The present study examined the effects of applying a pedagogical agent as a learning companion for supporting the cognitive process of learners to decrease their extraneous cognitive load. In the experimental condition, a pedagogical agent provided attention cueing to foster the cognitive process of selecting relevant information and to support the learners in acquiring knowledge on biological concepts in a multimedia learning environment. The findings indicate a general positive effect from the pedagogical agent on learning and a significant negative correlation between learning performance and cognitive load. In addition, an eye-tracking system was employed to investigate the eye movements, including the number of fixations, fixation time, and scan path, of students with high prior knowledge and students with low prior knowledge. Compared with the students with low prior knowledge, the students with high prior knowledge exhibited higher fixation densities on critical information.