Background: Gender-based violence (GBV) is an increasing social problem worldwide, but it has been neglected despite its high relevance to women’s health. In this study, we aim to assess the coronavirus disease 2019 (COVID-19) pandemic impact on GBV incidence in Peruvian, determine the physical violence prevalence and its associated factors among GBV victims. Methods: We assessed the impact of the COVID-19 pandemic on the GBV weekly incidence by fitting an autoregressive integrated moving average model. Additionally, we assessed the physical violence prevalence and its associated factors by fitting a multivariate Poisson regression model with a link log and robust variance. Results: We analyzed 588,587 cases of women victims of GBV and calculated an annual GBV incidence of 518, 714, 958, 596, and 846 cases per 100,000 women during the years 2017-2021, respectively. During the COVID-19 pandemic, the observed GBV weekly incidence went significantly below the forecasted GBV weekly incidence since 2021. Overall, most GBV cases were of middle to high-risk (76%), regular (75%), and verbal (82%) violence. Most victims were single (81%), rural (75%), mothers with children (60%), who did not complete high school (54%). Most aggressors were men (81%), paid workers (77%), had completed high school education (63%), and partner of their victims (58%). Around 44% of the victims suffered physical violence and its main associated factors were aggressor’s school education (adjusted prevalence ratio = 0.89; 95% confidence interval: 0.88-0.89), aggressor’s age <40 years old (1.30; 1.29-1.30), aggressor’s paid job (0.99; 0.98-0.99), prior violence report (1.27; 1.26-1.27), victim’s age <40 years old (1.23; 1.22-1.24), and victim non-Peruvian citizenship (1.04; 1.01-1.07). Conclusions: GBV is endemic in Peru, but the COVID-19 pandemic reduced its burden significantly in 2020-2021. Several characteristics of the cases, victims, and aggressors have changed over time, offering new opportunities for implementing interventions to address this social problem.