This study investigates the impact of generative artificial intelligence (GenAI) tools on the metacognitive development and academic performance of secondary school students using a quantitative, quasi-experimental design. Conducted over a 12-week intervention period, the study involved 120 Grade 9 students from an urban SSC-affiliated school in India. The participants were divided into control (traditional instruction) and experimental (AI-assisted instruction) groups. The experimental group engaged with four GenAI tools ChatGPT, Google Gemini, Microsoft Copilot, and QuillBot—integrated into science and English language instruction. Data were collected using the Metacognitive Awareness Inventory (MAI) and subject-specific academic achievement tests, administered pre- and post-intervention. The results revealed statistically significant improvements in both metacognitive awareness and academic performance among the experimental group. Paired sample t-tests and ANCOVA confirmed that students using AI tools demonstrated greater gains in metacognitive regulation and knowledge of cognition, as well as higher scores in science and language subjects, compared to the control group. These findings highlight the effectiveness of GenAI in fostering self-regulated learning and improving academic outcomes. The study addresses a critical gap in existing literature by providing structured, school-based evidence on AI-enhanced cognitive development in adolescents. The results have significant implications for curriculum design, teacher training, and policy, advocating for the ethical and pedagogically guided integration of GenAI tools into secondary education.