A 24-day old female Nigerian neonate presented with protracted vomiting, fever and dehydration but without palpable abdominal tumour or visible gastric peristalsis. There was no derangement of serum electrolytes. The initial working diagnosis was Late-Onset Sepsis but abdominal ultrasonography showed features consistent with the diagnosis of IHPS. This case report highlights the atypical presentation of this surgical condition and the need to investigate cases of protracted vomiting in the newborn with at least, ultrasonography to minimize complications and reduce the risk of mortality in a resource-poor setting.