Abstract Objectives Jejunal atresia and associated intramural calcification are a rare phenomenon, only few cases have been reported. Jejunal atresia is an antenatal developmental defect causing intestinal obstruction in newborns. In most of the cases, the condition is diagnosed by fetal ultrasound during the period of third trimester. We are reporting a case of neonatal jejunal atresia associated with intramural calcification and extensive foreign body reaction. Methods A baby girl was born at a gestational age of 36 weeks, 4 days through spontaneous vaginal delivery with a weight of 2.99 kg. The significant maternal history was gestational diabetes. The baby was diagnosed with jejunal atresia by antenatal ultrasound and received gastric suction immediately after delivery. About 200 mL of dark green fluid was suctioned from the stomach. Postnatal x-ray demonstrated significant distension of bowel loops and stomach. The baby underwent exploratory laparotomy with congenital atresia repair. Morphologically, the proximal portion of jejunum was dilated and small portion of distal segment of jejunum appeared to have type IIIB atresia. The atretic portion was examined grossly and processed as paraffin-embedded tissue for microscopic examination. Results The atretic segment was about 1 cm long, the serosal surface demonstrated foci of hemorrhage, and the wall was thickened. Microscopically, the atretic segment and adjacent area showed chronic inflammation, extensive foreign body type giant cell reaction, and abundant intramural calcification. Conclusion Some hypothesize that intramural calcification in conjunction with foreign body giant cell reaction associated with multifactorial events including vascular insults during the prenatal period. However, there are no studies directed to elucidate the precise pathogenesis of this combination of findings in the intramural location.