This paper presents an analytical study on the impact of science denial on classroom learning outcomes in India, using multilevel statistical modeling to analyze data across various educational settings. Science denial, a growing phenomenon fueled by misinformation and cultural biases, poses a significant threat to the integrity of education. This research aims to quantify the effects of science denial on student performance, particularly in subjects such as biology and environmental science. Data were collected from a diverse sample of schools across urban and rural regions in India, considering variables such as socio-economic status, teacher qualifications, and access to resources. The multilevel analysis reveals significant disparities in learning outcomes, with science denial contributing to lower academic performance and increased misconceptions among students. The study provides actionable insights for educators and policymakers to mitigate the negative impact of science denial through targeted interventions and curriculum reforms. These findings are crucial for preserving scientific literacy in Indian classrooms, ensuring that students are equipped with the critical thinking skills necessary to navigate an increasingly complex world.