BackgroundGender-based violence is a serious public health concern and affects a large number of women and girls in humanitarian emergencies. Despite this, there is a dearth of the summary data to address the issue. Therefore, this study aimed to assess the estimated pooled magnitude and factors associated with gender-based violence among refugees and internally displaced women in Africa.MethodsPubMed/MEDLINE, Google Scholar, African Journals OnLine, PsycINFO, and EMBASE were among the databases that were used to search the primary articles. The reviewed papers were articles that evaluated the prevalence and contributing variables of gender-based violence against refugees and internally displaced women in Africa. We extracted the data using a Microsoft Excel spreadsheet, which we exported into Stata version 14 for further analysis. The I2 test was applied to identify statistical heterogeneity. We used a random effect meta-analysis methodology because of the heterogeneity. A funnel plot and Egger’s weighted regression test were used to examine publication bias.ResultsThis systematic review and meta-analysis reviewed 17 primary studies with a total of 6,161 refugees and internally displaced women in Africa. The findings of this study revealed that the estimated pooled prevalence of gender-based violence among refugees and internally displaced women was determined to be 48.20% (95% CI: 39.28, 57.12). Young age (AOR = 3.68, CI: 2.63, 5.14), alcohol consumption (AOR = 2.53, CI: 1.56, 4.11), and having no social protection (AOR = 3.21, CI: 2.22, 4.63) were factors significantly associated with gender-based violence.Conclusions and recommendationsThe present study showed that almost half of refugees and internally displaced women residing in Africa were survivors of gender-based violence. Younger women, alcohol users, and those without social protection were more likely to experience gender-based violence. Therefore, it is recommended that accessible information about the consequences of gender-based violence and early intervention for survivors be provided, taking these factors into consideration.