The flipped classroom method has recently become popular in biology education. However, there is a lack of systematic and quantitative assessments on the efficiency of teaching medical microbiology using this novel approach. In this study, we performed a meta-analysis to explore the flipped classroom method's effects versus those of traditional lectures in medical microbiology education. Six electronic databases, including PubMed, Web of Science, ERIC, China National Knowledge Infrastructure (CNKI), Wanfang Data, and Chinese Scientific Journals Database, were searched to obtain relevant articles from the first publication on this topic up to March 2021. Study selection, data extraction, and quality estimations were conducted to analyse the effects. A total of 13 studies were included in this meta-analysis, with the results revealing a significantly improved effect within the flipped classroom model on students' theoretical [SMD = 0.56, 95% CI (0.28, 0.84), p < 0.0001] and practical examination scores [SMD = 0.70, 95% CI (0.19, 1.20), p = 0.007]. In terms of its teaching effects, the flipped classroom approach improves students' learning interest, self-study abilities, knowledge mastery, and satisfaction, but does exacerbate their learning burden. The flipped classroom method possesses multiple advantages when compared to traditional lectures in medical microbiology education, but does increase the burden experienced by students.