Development of hypertrophic pyloric stenosis (HPS) after a few weeks of repair of an oesophageal atresia (OA) and tracheo-oesophageal fistula (TOF) is a rare condition in early infancy. Although vomiting or feeding intolerance in operated cases of OA+TOF are attributed to oesophageal stricture, gastro-oesophageal reflux and oesophageal dysmotility, it may also be caused by HPS. Herein, we report a newborn infant who had OA and TOF operation on day 2 of life and diagnosed to have HPS at 15th day of age. Even though it is a rare anomaly, HPS should be kept on mind in the presence of persistent vomiting following repair of OA.