This study aimed to estimate the prevalence of current smoking among medical students in mainland China through a systematic search across six electronic databases for English or Chinese studies published before May 25, 2018. A total of 79 studies were included; 26 had a high risk of bias. The overall pooled prevalence of current smoking was 10.93% (7460/68253; 95%CI: 0.09%, 13.08%, I2 = 98.6%). This study found a decreasing prevalence of current smoking over the period studied (survey year range of 1988–2014). More specifically, the current smoking prevalence in males decreased progressively across time, while the prevalence in females remained relatively constant. The overall prevalence in the west was higher than in the middle or east of mainland China (p = 0.0061). The overall prevalence of current smoking increased with year in school (p = 0.0028). The present study provides a comprehensive synthesis of current smoking prevalence among medical students in mainland China. Although there have been some improvements in the status of tobacco use among medical students, given the leading role of physicians in tobacco control, sustained efforts are needed to curb the tobacco epidemic among medical students.