Notwithstanding the growing advantages of incorporating Augmented Reality (AR) in science education, the pedagogical use of AR combined with Pedagogical Agents (PAs) remains underexplored. Additionally, few studies have examined the integration of Generative Artificial Intelligence (GAI) into science education to create GAI-enhanced PAs (GPAs) that enrich the learning experiences. To address these gaps, this study designed and implemented a GPA-enhanced 5E model within AR environments to scaffold students' science learning. A mixed-methods design was conducted to investigate the effectiveness of the proposed approach on students' academic achievement, cognitive load, and their perceptions of GPAs as learning aids through using the 5E model. Sixty sixth-grade students from two complete classes were randomly assigned to either an experimental group engaged in AR science learning with a GPA-enhanced 5E approach or a control group that followed the traditional 5E method. The findings revealed that the GPA-enhanced 5E approach in AR environments significantly improved students' academic achievement and decreased cognitive load. Furthermore, students in the experimental group reported positive perceptions of the GPA-enhanced 5E method during the AR science lessons. The findings offer valuable insights for instructional designers and educators who leverage advanced educational technologies to support science learning aligned with constructivist principles.