Objective To estimate the incidence of suicidal ideation of Chinese medical students in mainland China over the past ten years by meta-analysis, so as to provide references for suicide prevention and mental health education in Chinese medical students. Methods PubMed, CNKI, WanFang Data and CBM databases were searched for studies investigating the prevalence of suicidal ideation among Chinese medical students in mainland China from January 1st, 2007 to 31st May, 2017. After study selection according to inclusion and exclusion criterion, data extraction and quality assessment, meta-analysis was conducted using Stata 12.0 software. Heterogeneity was evaluated by performing subgroup analyses and meta-regression. We also used sensitivity analysis to determine the influence of individual studies on the overall prevalence estimates. Results A total of 30 studies with 58 757 participants were included, the individual-study incidence of suicidal ideation ranged from 0.84% to 41.35%, with significant between-study heterogeneity detected (I2=99.1%, P<0.001), and the pooled incidence by random-effects model was 12.51% with 95%CI 9.72% to 15.60%. Univariate and multivariate meta-regression revealed that instruments were related to heterogeneity (P<0.01), but other study-level covariates did not contribute to heterogeneity (P>0.1). Conclusion The incidence of suicidal ideation among medical students in mainland China is relatively high, calling more attention to this concern and actions in response for suicide prevention and mental health education in Chinese medical students.