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Gender-based violence is a public health issue. The prevalence of gender-based violence is high in Sub-Saharan Africa. Therefore, this study aims to produce an overall summary estimate on the prevalence of gender-based violence according to different types and its risk factors among female youths in educational institutions of Sub-Saharan Africa. Studies published in English between 2000 and 2017 were identified by searching electronic databases such as MEDLINE, CINAHL, EMBASE, PsychINFO, and other relevant data bases. Three reviewers independently extracted the data and assessed the quality of studies using the Loney guidelines. The pooled prevalence of gender-based violence and type of GBV was computed using STATA software version 14, and between studies heterogeneity was tested using Cochran’s Q test and I2 statistics. Meta-regression analyses were done to identify factors associated with GBV estimates. A total of 1377 articles were produced from different databases, and a final 24 articles were included in the review. The overall prevalence of gender-based violence ranged from 42.3% in Nigeria to 67.7% in Ethiopia. The lifetime prevalence of sexual violence ranged from 4.3 to 76.4%, physical violence ranged from 7.4 to 66.1%, and emotional violence prevalence ranged from 26.1 to 50.8%. The overall pooled prevalence of lifetime GBV (n = 7 studies) was 52.83% [95% CI 39.54–65.90%, I2 = 99.1, P < 0.00]. The pooled estimate of sexual violence (n = 23), 26.22% [95% CI 19.48–33.57%, I2 = 99.39, P < 0.00], physical violence (n = 9), 18.86% [95% CI 10.96–28.3%, I2 = 98.98, P < 0.00], and emotional violence (n = 5), 27.06% [95% CI19.57–35.28%], I2 = 97.1, P < 0.00]. The review showed that gender-based violence was significantly associated with place of residence, witnessing parental violence, substance abuse, marital status, and educational status. The overall prevalence of overall gender-based violence, sexual, physical, and emotional violence was high in Sub-Saharan Africa. The lowest prevalence of GBV was observed in Nigeria, and it was highest in Ethiopia. However, the results should be interpreted with caution because of high between studies heterogeneity. Evidence from the review part revealed GBV was significantly associated with place of residence, witnessing parental violence, substance abuse, marital status, and educational status. The Sub-Saharan African countries should develop a comprehensive educational institution-based prevention strategy and effective interventions to mitigate gender-based violence and to specifically achieve the SDG5. PROSPERO CRD4201073260