Introduction: Windsock deformity of the duodenum is a rare congenital anomaly . When associated with intestinal malrotation, the duodenal web may be easily overlooked, as both conditions present with similar features of obstruction. This overlap makes early diagnosis and appropriate surgical management particularly challenging. Case Report: A 15-day-old male neonate (34 weeks, 2050g) presented with a history of projectile bilious vomiting and he had gradual gaseous abdominal distension. Initial ultrasound (USS) of the abdomen showed no features of pyloric stenosis. Upper Gastrointestinal(UGI) contrast study showed evidence of partial duodenal obstruction due to possible malrotation. Therefore, Ladd’s procedure and Inversion Appendicectomy were performed. During the procedure, a complete non-rotation with multiple Ladd’s bands obstructing the duodenum was found. However, bilious vomiting persisted after the surgical intervention. The second UGI contrast study was done on day 34 of life and it showed evidence of obstruction at the distal 2nd part of the duodenum. Hence a laparotomy was done and a few adhesions over the duodenum were seen. There was a duodenal membrane with perforation, which was identified as Windsock Deformity , where a Nasogastric tube cannot be passed through it. The release of the windsock membrane was performed. The baby clinically improved with tolerating feeds and he was discharged home. Discussion: This case highlights the importance of persistent evaluation in neonates with ongoing bilious vomiting despite initial surgical correction. Dual pathology can coexist, and timely re-exploration with definitive surgical management is crucial to achieve complete resolution and ensure favorable clinical outcomes.