Abstract Background General and regional anesthesia are the two main techniques used in cesarean section. Regional anesthesia is preferred, but under certain circumstances, such as by patient request and in patients with back deformities, general anesthesia is the only option. Commonly used induction agents include thiopental, ketamine, and propofol, depending on availability and the maternal clinical condition. The objective of this study was to investigate the effects of thiopental and propofol on the neonatal Apgar score and maternal recovery time following emergency cesarean section in order to determine the superior agent for mothers and neonates. Methods This single-blinded randomized clinical trial included 150 ASA I and II patients block-randomized equally between the two study arms. Pregnant women at term scheduled to undergo cesarean section and their neonates were enrolled. The primary outcomes were the Apgar scores through 10-min postpartum, resuscitation requirement, and admission to the neonatal intensive care unit. The secondary outcome was the maternal recovery times. Results At 0 min (umbilical cord clamp time), 43 (57.3%) neonates in the propofol group had an Apgar score