Background <p>Cesarean section performed during the second stage of labor is technically challenging and associated with higher maternal and neonatal morbidity. This study aimed to assess adverse maternal and perinatal outcomes for women who have a cesarean section performed during the first and second stages of labor at Hawassa University Comprehensive Specialized Hospital.</p> Methods <p>An institution-based comparative cross-sectional study was conducted from May to November 2024 among 278 term women who underwent intrapartum cesarean delivery. Among these, 193(69.4%) had first-stage cesarean delivery, and 85(30.6%) had second-stage cesarean section. Data were collected using structured questionnaires and medical record review. Multivariable logistic regression analysis was performed to identify factors associated with adverse maternal and perinatal outcomes.</p> Results <p>During the study period, there were 1434 deliveries, of which 716 were cesarean sections, yielding a cesarean delivery rate of 49.9%. The overall rate of adverse maternal and perinatal outcomes was 24.5% and 29.1%, respectively. Compared with the first-stage cesarean section, second-stage cesarean delivery is associated with increased odds of adverse maternal outcomes (AOR = 4.20, 95% CI: 1.95–9.05) and adverse perinatal outcomes (AOR = 3.05, 95% CI: 1.65–5.65).</p> Conclusion <p>Cesarean section performed during the second stage of labor was significantly associated with adverse maternal and perinatal outcomes. During the second stage of cesarean delivery, the obstetric team’s preparedness for potential intraoperative complications and immediate neonatal resuscitation should be strengthened.</p>