Most of the learning institutions even before the global pandemic are using a blended learning strategy. One of the most promising and leading blended-strategy today is the Flipped Classroom Model (FCM). FCM, often called as inverted classroom or reversed instruction, is a teaching model where the content of the study is given outside the classroom and homework is done inside the classroom. Previous researches yields different results when FCM is compared with traditional learning in enhancing students’ academic performance. To address the problem, a meta-analysis has been conducted. In this study, 15 articles were chosen to be meta-analyzed. The researchers used the PRISMA model in conducting the meta-analysis and the Meta-essentials for data analysis. The analysis yields a p-value of 0.000 which means that there is a statistical significant effect by the intervention FCM to the academic performance of the students. The hedges’ g value of 0.93 has a verbal interpretation of large effect. Through subgroup analysis, it was found that FCM has a positive effect on the academic performance of the students in the subjects Physics and Mathematics with a p value of 0.000. This is also true in the subgroup, Geographical Location (Eastern and Western Countries), that yields a p-value of 0.000. Further, a moderator analysis on class size and intervention duration was also conducted. A significant p-value was found on the moderator implementation duration but not significant in the moderator class size. The analysis favors the longitudinal use of Flipped Classroom Model on enhancing student’s academic performance over Traditional Lecture Model in the subjects Physics and Mathematics regardless the class size of the students and the regions where the studies were conducted.