This meta-analysis evaluated the effectiveness of inquiry-based learning (IBL) on improving students' conceptual understanding in science and mathematics. The study systematically reviewed 12 empirical studies with 14 effect sizes involving 786 students across various countries, educational levels, and disciplines. These studies were selected using the PRISMA (2020) guidelines and the developed inclusion and exclusion criteria based on publication years (2014-2024), levels of IBL employed, and measures of students' conceptual understanding in science and mathematics. The results showed that IBL had a significant positive effect size (g = 0.913) on improving students' conceptual understanding, particularly in senior high school (g=1.176) and mathematics (g=1.191). Open inquiry had the greatest effect size (g=1.530), emphasizing the importance of student autonomy in learning. The findings support the broader implementation of IBL in educational curricula and teachers' training programs to foster a more student-centered learning environment that encourages inquiry, critical thinking, and deeper conceptual understanding in science and mathematics, which are essential for success in the 21st century. Recommendations include customizing IBL to students' needs and further research on diverse IBL strategies and their impact on student outcomes.