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.