The integration of Generative Artificial Intelligence (GenAI) in STEM education is transforming how students engage with learning. AI-driven tools support personalized learning, automate problem-solving, and enhance higher-order thinking skills. However, its impact on students’ computational thinking (CT) skills and learning dispositions remains underexplored. This study evaluates the impact of Generative AI on CT skills and learning disposition among Malaysian secondary school students in Form One Science. A quasi-experimental research design was employed, dividing students into AI-assisted and traditional learning groups. Validated assessment tools were used to measure CT skills and dispositions. Data were analyzed using descriptive statistics and one-way MANOVA to determine significant differences between the groups. Findings show AI’s positive influence on student disposition and CT skills, particularly within an Inquiry-Based Science Education (IBSE) framework. However, challenges such as over-reliance on AI and technological disparities must be addressed. This study informs educators and policymakers about AI’s pedagogical, ethical, and technological implications in STEM education.