<p>Inquiry-based learning has been a promising method in science curricula and many research projects. However, learners often struggle with low scientific inquiry skills, performance, and self-efficacy. To address these problems, this study aims to facilitate inquiry-based learning through generative artificial intelligence (GenAI) technologies. The current study compared three approaches to facilitating inquiry-based learning. In total, 120 pupils from three classes in Grade 5 participated in this study. Each was assigned to either experimental group 1, which used GenAI-based pedagogical agents to carry out inquiry-based learning, experimental group 2, which used GenAI-based chatbots to conduct inquiry-based learning, or the control group, which used a traditional learning platform to conduct inquiry-based learning. The results indicated that the knowledge gains, scientific inquiry skills, inquiry-based learning performance, and self-efficacy of the two experimental groups were substantially greater than those of the control group. There were no significant differences in knowledge gains, scientific inquiry skills, inquiry-based learning performance, or self-efficacy between experimental group 1 and 2. This study made two core contributions. First, it elucidates the significant influence of GenAI on scientific inquiry skills and inquiry-based learning performance. Second, it examines actionable strategies for the effective integration of GenAI within inquiry-based learning. Therefore, the present study advocates for the application of GenAI as a transformative tool to advance future inquiry-based learning practice.</p>