In recent years, the flipped classroom has emerged as an alternative pedagogical model in pharmacy education, combining digital pre-class learning with in-person, student-centered classroom activities. Despite its growing adoption, uncertainty remains regarding whether this instructional approach offers clear advantages over conventional lecture-based teaching. This meta-analysis was undertaken to critically assess and quantify the comparative effectiveness of flipped classroom instruction versus traditional lectures, aiming to provide a more definitive evaluation of its educational impact within pharmacy curricula.A systematic search strategy was applied to seven electronic databases, including the Cochrane Library, PubMed, Embase, ScienceDirect, Web of Science, China National Knowledge Infrastructure (CNKI), and the Chinese Biomedical Literature Service System (SinoMed). Studies were considered eligible if they reported objective measures of academic performance and directly compared flipped classroom formats with traditional instructional methods. Effect sizes were synthesized using standardized mean differences (SMDs) and corresponding 95% confidence intervals (95% CIs).The analysis incorporated 22 eligible studies, representing 28 independent comparisons and a total sample size of 4,379 students. Overall methodological quality was variable, with many studies demonstrating an elevated risk of bias. Meta-analytic findings indicated that students exposed to flipped classroom instruction achieved significantly higher academic performance than those receiving traditional lectures, and no significant publication bias was detected. Further subgroup analyses confirmed the superiority of the flipped classroom across different outcome measures and educational levels.The findings of this meta-analysis indicate that flipped classroom pedagogy is associated with meaningful improvements in learning outcomes in pharmacy education compared with conventional teaching approaches. To maximize these benefits, future instructional designs should prioritize the strategic use of educational technologies and foster active, interactive learning environments.