Background: Sexual violence against female children is considered an important public health problem. However, there are currently no clear prevalence rates across the globe on which to base measures to protect these children. The objective of this study is to systematically summarize the prevalence of sexual violence against female children. Methods: We conducted a comprehensive search of the PubMed, Embase and Web of Science databases from their inception through April 2021 for pertinent studies reporting the prevalence of sexual violence against female children. The prevalence rate was estimated using a random-effects meta-analysis. The heterogeneity was evaluated using I-2 statistic. Differences by study-level characteristics were estimated through subgroup analysis and meta-regression. Results: A total of 28 cross-sectional studies were included (a total of 30,524 participants). The pooled sexual violence rate against female children was 0.24 (95 % CI = 0.20-0.27). Groups comparisons revealed that sexual violence rates obtained from 1981 to 2000 (0.28, 95 % CI = 0.21-0.36) were higher than those obtained from 2001 to 2020 (0.21, 95 % CI = 0.16-0.25), that rates were higher for female children from developed countries (0.25, 95 % CI = 0.20-0.29) than for those from developing countries (0.21, 95 % CI = 0.14-0.27), the rates for surveyed adults (0.22, 95 % CI = 0.17-0.28) than for surveyed female children (0.18, 95 % CI = 0.10-0.26), and that rates for those <= 15 years of age (0.10, 95 % CI = 0.01-0.20) were much lower than those for older children. Conclusions: Nearly a quarter (24 %) of female children have been victims of sexual violence. Prevention strategies should be developed urgently to protect female children from aggression.