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Esophageal atresia (EA) and tracheoesophageal fistula (TEF) are surgically correctable congenital anomalies with reported surgical common complications such as anastomotic leaks, recurrent TEF, and esophageal strictures; however, phrenic nerve injury (PNI) is a very rare but possible complication which we have highlighted in our case report. Here, we report a baby girl operated for long-gap EA and TEF having respiratory distress and failed attempts to wean off oxygen support. Serial chest X-rays showed elevated right hemidiaphragm, whereas ultrasound thorax confirmed our diagnosis of right PNI causing diaphragmatic palsy. Conservative management with the hope of spontaneous recovery failed, so diaphragmatic plication was done at 5 weeks from index surgery. Postplication, the baby was weaned off oxygen and pressure support the very 1st day and had improved respiratory physiology.