Background: Esophageal atresia and tracheoesophageal fistula (EA/TEF) is a known correctable anomaly of the esophagus, and its prognosis depends on multiple factors. Studies investigating the EA/TEF post-operative outcomes among the Iranian population are limited to small sample sizes, and the current prevalence of coexisting anomalies and predictors of poor prognosis in the Iranian population is still unclear. Objectives: This study aimed to investigate the predictors of in-hospital mortality in neonates with EA/TEF at our center within a 12-year period. Methods: In this retrospective cohort study, we investigated neonates with EA/TEF admitted/referred to a tertiary referral center in Tehran, Iran, from March 2008 to April 2020. Neonates with chromosomal anomalies or age > 10 days at operation date were excluded. Baseline characteristics, associated anomalies, type of EA, and transmission distance were compared in the study population. We followed the neonates for incurring in-hospital mortality. Results: We included 233 neonates in the final analysis. The mean age at operation was 3.1 ± 1.7 days, and 111 (47.6%) cases were female. The most common EA type was type C (proximal esophageal atresia with distal fistula), with a prevalence of 94.4%. In this cohort, 23 (9.9%) cases had vertebral anomalies, anal atresia, cardiovascular malformations, trachea-esophageal fistula, renal and limb anomalies (VACTERL) association, and 29 (12.4%) cases died during the in-hospital course. Moreover, neonates with lower birth weight, gestational birth weight < 37 weeks, other coexisting anomalies, cardiovascular defects, and non-VACTERL anomalies were at higher risk of in-hospital mortality. In contrast, EA types and transmission distance did not increase the mortality risk. Furthermore, we measured a cut-off value of < 2575.0 g for birth weight to predict in-hospital mortality with 65.5% sensitivity and 61.3% specificity. Conclusions: Lower birth weight, prematurity (< 37 weeks), and coexisting anomalies, especially cardiovascular defects, were associated with an increased risk of in-hospital mortality in neonates after EA/TEF repair surgery.