Background: Cesarean section rates have been steadily increasing worldwide. Private health facilities are reported as being a major contributor to this rising rate in Latin America. Aim: To assess the prevalence and determinants of cesarean section rates among public and private health facilities in Peru. Methods: We performed a cross-sectional analytical study pooling the data of 52,215 women between 15 and 49 years of age from the 2015–2017 Peruvian Demographic and Family Health Survey (ENDES) database. Sociodemographic and pregnancy-related variables were used to construct adjusted logistic regression models for the indication of cesarean section. Findings: The prevalence of cesarean births was 73.0% (95%CI: 71.1–74.9) and 30.3% (95% CI: 29.6–31.0) in private and public health facilities, respectively. In private facilities, living in an urban area, having a higher educational level, being in the age group of 35–49 years, and having multiple pregnancies increased the probability of a cesarean section. In public health facilities, living in an urban area, having a higher wealth quintile, higher education level, older maternal age, birth order, newborn size and gender, type of pregnancy, language, and maternal height were all factors associated with cesarean section. Conclusion: The prevalence of cesarean section found in the present study was above the value recommended by the WHO (10%) for both public and private facilities. It is necessary to address the indiscriminate rise in the use of cesarean sections, developing strategies according to the type of health facility.