Background: Many advances have been made in managing neonates with esophageal atresia/tracheoesophageal fistula (EA/TEF). This resulted in a progressive decrease in mortality as a result of improved neonatal intensive care and neonatal mechanical ventilation; however, this is not the case in developing countries. Objectives: We aimed to evaluate the efficacy of postoperative ventilation in neonates with EA/TEF in Iraq as a developing country. Materials and Methods: It is a prospective study for all neonates with EA and/or TEF admitted to the pediatric intensive care unit (PICU) in Alkhansaa Teaching Hospital between December 2012 to December 2014. Forty operated neonates were randomly divided into two groups according to the record number of presentations (even = G1, odd = G2): Twenty patients (group l) had been assigned to be post-operatively on a ventilator as a routine protocol. While group 2 planned to be extubated in the theater. We evaluated the complications and mortality rates in two groups. Results: For 24 months, 40 neonates with EA/TEF were admitted to PICU; Thirty-two were operated on within 24 hours of life. There were no significant differences between the two groups regarding fetal maturity (p-value 0.490), gender, and weight. The mean period for mechanical ventilation was four days. Six neonates had tube mal-positioning complications, leading to lung collapse, hypoxia, and pneumonia (p-value 0.250). Anastomotic leaks occur in 10 neonates (five in each group) (p-value 0.642), which sometimes leads to sepsis (p-value 0.347). Trachea-malacia was recorded after weaning in 5 intubated patients (p-value 0.078). The mortality rate in G1 was 35%, while in group 2 was 25% (p-value 0.366). Conclusions: Although the study’s sample is small, it is recommended to avoid mechanical ventilation in the postoperative care of neonates with EA and/or TEF.