Vitelline veins are a pair of embryonic structures. The veins develop the portal vein system. Serious problems occur if the vitelline vein does not regress and becomes an aneurysm. Thrombus formation in the vitelline vein aneurysm could lead to portal vein thrombosis and portal hypertension unless promptly and correctly treated. Though vitelline vein aneurysm is an extremely rare anomaly, it rapidly progresses to portal vein thrombosis that requires prompt diagnosis and treatment. We reported a case of neonatal vitelline vein aneurysm and thrombosis that was cured by prompt operation.