Introduction Pre-operative management of neonates with esophageal atresia and tracheoesophageal fistula (EA/TEF) requiring positive pressure ventilation (PPV) support is clinically challenging. This study evaluates the safety, feasibility and value of flexible endoscopy with noninvasive ventilation and sustained pharyngeal inflation (FE-NIV-SPI) in diagnosis and placing a naso-tracheo-fistula-gastric (NTFG) tube before surgery. Methods A retrospective study conducted from 2017 to 2020 in neonates with Type-C EA/TEF and respiratory distress, where FE-NIV-SPI performed with NTFG tube placement before surgery. Results Five neonates were collected, one with duodenal atresia and one with transposition of great artery. At FE-NIV-SPI, median body weight was 2,399 g and mean age was 15.2 hours. Four neonates yielded severe (>80% collapsed) tracheomalacia. With this FE-NIV, all tracheal, fistulas and esophageal lumens could clearly assess and manage. All fistulas were less than 8mm proximal to carina with mean orifice width of 5 mm. All NTFG tubes placed successfully after confirmed the EA/TEF. Three neonates had co-intubated with nasal endotracheal tube and 2 neonates had received nasal prongs PPV. Mean procedural time of FE-NIV was 13.6±4.5 minutes. All neonates received gastric decompression and feeding via NTFG tubes for mean of 11.4±18.2 days and had stable pre-surgical courses. No adverse associated complication noted. Conclusion FE-NIV-SPI technique enables safe and accurate measurement of EA/TEF anatomy and placing NTFG tube. It could avert emergent gastrostomy, aid gastric decompression, feeding, and ETT intubation, improve PPV, provide pre-surgical stabilization and identify the fistula location during the surgical correction.