The data on the prevalence of kidney stones in mainland China are still lacking. We performed the present meta-analysis to assess the stone prevalence in mainland China from 1990 through 2016. A total of 18 articles were included. The pooled overall prevalence was 7.54% (95% CI, 5.94-9.15). The prevalence in age groups of < 20 years, 20-29 years, 30-39 years, 40-49 years, 50-59 years, and 60 years and older was 0.27%, 3.15%, 5.96%, 8.18%, 9.14%, and 9.68%, respectively, showing that it increased with age. Moreover, the prevalence was 10.34% in males and 6.62% in females, with an odds ratio (OR) of 1.63 [95% CI: 1.51-1.76], indicating that males are more likely to suffer from this disease than females. However, urban areas (6.03%, 95%CI: 3.39-8.68) and rural areas (7.48%, 95% CI: 3.39-11.57) did not differ in the stone prevalence rate (OR =0.84, 95% CI: 0.42-1.68). The prevalence in the year groups of 1991-2000, 2001-2010, and 2011 to date was 5.95%, 8.86%, and 10.63%, respectively, which indicated an increasing trend. Further high- quality surveys throughout mainland China are needed to confirm these findings.