Congenital tracheo-oesophageal fistula (TOF) occurs in 1 in 3000 births. Perioperative management for TOF repair requires co-ordination with a multi-disciplinary team, support from critical care units, and expertise in neonatal and cardiothoracic anaesthesia. Charlotte Maxeke Johannesburg academic hospital (CMJAH) is a quaternary referral centre that serves the regional community of Johannesburg, in Gauteng, South Africa. The aim of this research was to describe the perioperative outcomes of neonates undergoing surgical TOF repair at CMJAH. Factors in the preoperative, intra-operative, and postoperative management were considered to find relationships with the perioperative outcomes. A retrospective single institution study was conducted with a population of 38 neonates who underwent congenital TOF repair from 1 January 2015 to 31 March 2020 at CMJAH. Descriptive statistics were used to describe the biodata using percentages, median, and inter-quartile ranges. An in-depth description of neonates that died was performed. A total of 38 neonates diagnosed with TOF/OA were operated on during the study period. The mortality rate was 15.8%. No deaths occurred intraoperatively. In addition, 52.6% of the neonates had a prolonged stay in ICU, 44% had a delay in the initiation of feeds, 65% developed sepsis, and 36.8% had surgical related complications. CPR was required in 1 neonate, hypoxia leading to bradycardia in 10, and hyperlactataemia in 9 neonates. Inotropic support was required in 6 neonates, and vasopressor support in 4. Blood product transfusion were necessary for 9 neonates. The in-hospital mortality of TOF repair was better than that reported in other African countries and worse than international findings. In-hospital morbidity was burdened by respiratory illness and sepsis. Areas where management could be improved include widespread foetal anomaly scanning, incorporation of bronchoscopy, and preoperative respiratory optimisation.