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Abstract Background To address the challenges of limited national data on the prevalence and nature of violence experienced by children, Rwanda conducted, in 2015–2016, the first National Survey on Violence among female and male children and youth aged 13–24 years. To further contribute to these efforts to fill existing data gaps, we used the Rwanda survey data to assess the prevalence and predictors of physical violence (PV) in children aged 13–17. Methods A nationally representative sample of 618 male and 492 female children were analysed. Nationally representative weighted descriptive statistics were used to analyse the prevalence of PV self-reported by children, and logistic regression models were applied to investigate its predictors. Results Sixty percent of all children, including 36.53% of male and 23.38% of female children, reported having experienced any form of PV in their lifetime. Additionally, 21.81% of male children and 12.73% of female children reported experiences of PV within twelve months before the survey date. Older children (OR: 0.53 [0.40–0.72]), female children (OR: 0.43 [0.31–0.58]), and children not attending school (OR: 0.48 [0.31–0.73]) were less likely to be physically abused. However, sexually active children (OR: 1.66 [1.05–2.63]), children in households from the middle wealth quintile (OR: 1.63 [1.08–2.47]), children living in a larger family (OR: 1.55 [1.07–2.26]), and children who reported not feel close to both biological parents (OR: 2.14 [1.31–3.49]) had increased odds of reporting physical violence. Conclusion Higher rates of PV in children attending school were the key finding. There is an urgent need to design and implement particular national interventions to prevent and reduce the incidence of PV in schools in Rwanda. PV was also associated with poor parent-child relations. Parents and other adult caregivers should be sensitised to the consequences of PV on children and be urged to adopt positive parenting practices.