Background: Tracheoesophageal fistula (TEF) is a rare congenital anomaly with significant morbidity and mortality, particularly in resource-limited settings. Prognosis is influenced by factors such as birth weight, associated anomalies, and postoperative complications. Objective: To evaluate the diagnosis, outcome, and prognosis of patients with tracheoesophageal fistula at a tertiary care centre. Methods: A retrospective and prospective study was conducted in the Department of General Surgery over five years (2020–2024). A total of 46 neonates diagnosed with TEF were included. Data on demographics, clinical presentation, associated anomalies, surgical management, and postoperative outcomes were analyzed. Statistical analysis was performed using SPSS version 25. Results: The mean age at presentation was 1.91 days, and mean birth weight was 2.04 kg. Type C TEF was the most common (93.5%). Associated anomalies included cyanotic congenital heart disease (23.9%) and spinal anomalies (28.3%). Postoperative ventilator support was required in 58.7% of cases. Overall mortality was 52.2%, with ventilator-associated pneumonia (21.7%) and sepsis (19.6%) being the leading causes of death. Survival was poorest in neonates weighing <1.5 kg and those with associated cardiac anomalies. Conclusion: Outcomes in TEF are strongly influenced by low birth weight, associated congenital anomalies, and postoperative infectious complications. Early diagnosis, multidisciplinary care, and improved neonatal intensive care support are essential to reduce mortality, particularly in high-risk groups.