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Aperta lipomyelomeningocele (LMMC) is a form of open spinal dysraphism often associated with Chiari II malformation. Infantile hypertrophic pyloric stenosis (IHPS), the leading surgical cause of gastric-outlet obstruction in early infancy, has rarely been reported alongside LMMC and Chiari II. We present a term male neonate who underwent early repair of lumbosacral LMMC and later ventriculo-peritoneal (VP) shunting for post-haemorrhagic hydrocephalus. Persistent non-bilious vomiting despite functional shunting led to imaging that confirmed IHPS. The infant required a phased surgical approach, combining Ramstedt pyloromyotomy with simultaneous VP shunt revision, followed by extended multidisciplinary rehabilitation. The coexistence of these three distinct congenital anomalies produced overlapping symptoms and delayed IHPS diagnosis. This case emphasises the need for vigilant reassessment of ongoing gastrointestinal symptoms in children with neural tube defects and explores embryological links between these conditions. Recognising such rare associations is vital for timely intervention and improved outcomes.