<p>The current study aimed to explore the influence of pedagogical agents and visual cues on students’ deep learning within a virtual reality setting by evaluating the effects on various factors, including learning outcomes, intrinsic motivation, cognitive load, learning engagement, and cognitive processing metrics. The investigation utilized a 2 × 2 factorial between-subjects experimental design, wherein 72 participants were randomly assigned to one of four conditions resulting from the fully crossed manipulation of pedagogical agent (present vs. absent) and visual cue (present vs. absent). The Tobii Pro X3-120 eye-tracking device was utilized for the assessment of learning engagement., while Emotiv EPOC Flex EEG was utilized to assess cognitive processing. Learning outcomes were assessed through a learning performance test, while intrinsic motivation and perceived cognitive load were evaluated using self-report instruments. Two-way ANOVA analyses revealed that the presence of visual cues has marked improvement on intrinsic motivation, learning engagement, and cognitive processing among participants. The combination of pedagogical agents and visual cues yielded a synergistic effect and significantly optimized learning outcomes. Noticeably, the combination of pedagogical agents and visual cues can effectively stimulate students’ intrinsic motivation, encouraging them to invest more cognitive resources in the learning process and increasing the likelihood of successful long-term memory encoding, which in turn leads to better learning outcomes. The findings of this study, derived from multiple data analysis, provide valuable insights for the design of VR settings that effectively foster students’ deep learning.</p>