Background: Jejunal atresia is a rare cause of neonatal intestinal obstruction, often diagnosed postnatally. Meconium plug syndrome, typically a functional obstruction of the colon, can occasionally mimic lower gastrointestinal anomalies antenatally. Coexistence of these two conditions is extremely rare, especially in the absence of cystic fibrosis. Case Report: A 36-week female neonate was born to a primigravida mother with severe preeclampsia and fetal growth restriction. Antenatal ultrasound suggested large bowel obstruction or imperforate anus. Postnatally, the baby presented with abdominal distension and failure to pass meconium. A long, 16 cm meconium plug was expelled after per-anal saline and mucolytic washes. Despite initial relief, imaging continued to show persistent obstruction. Exploratory laparotomy on day 4 revealed Type I jejunal atresia 30 cm distal to the DJ junction. A 20 cm segment was resected, followed by primary jejunojejunal anastomosis. Despite surgical correction, the neonate succumbed to sepsis on day 7 of life. Conclusion: This case highlights a rare coexistence of jejunal atresia and an unusually long meconium plug, leading to antenatal misdiagnosis. Accurate prenatal identification of intestinal atresia is crucial for timely intervention, appropriate counselling, and improving neonatal outcomes.