This study was designed to examine whether embodied agent integrated with the pedagogical approach of learning by asking questions impacts lower academic ability students' perceived science self-efficacy beliefs, immediate and delayed retention and whether the students' cognitive styles interact with the treatment condition in the outcome measures. The participants learned the topic Energy in Year Five Science over a period of one week either through the experimental condition of embodied agent with students' commonly asked questions (EA with SCAQ) or the comparison condition of voice over with students' commonly asked questions (VO with SCAQ). The findings showed that embodied agent significantly impacted students' performance in delayed retention and perceived science self-efficacy beliefs. Significant interaction effect was also found between embodied agent condition and field dependent learners in the measures of delayed retention and perceived science self-efficacy beliefs. However for the measure of immediate retention, the students profited equally from the web-based environment, independent of the treatment conditions and cognitive styles. Overall this study extended knowledge to designers of pedagogical agent environment in building a user interface that allows learning with an understanding of HCI principles and students' cognitive styles.