A rare case of isolated superior mesenteric venous thrombosis (MVT) after endoscopic variceal band ligation (EVL) is reported. A 64-year-old woman with a history of idiopathic portal hypertension presented at the emergency room with vomiting, increasing cramping abdominal pain, and low-grade fever. She had undergone EVL for esophageal varices 4 months before and had had intermittent attacks of mild abdominal pain after the EVL. Ultrasonogram of the abdomen demonstrated marked concentric wall thickening of the ileal loop. Enhanced computed tomographic (CT) scan revealed a central lucency in the lumen of the superior mesenteric vein, surrounded by a high-density vein wall, corresponding to a thrombus. An isolated MVT and venous collateral network in the splanchnic area were confirmed by angiography. Supportive therapy, i.e., water and electrolyte replacement, and anticoagulation improved the clinical condition and radiologic status. This case of MVT after EVL suggests a possible relationship between EVL and MVT. It is necessary for clinicians to be aware of this relationship for the early diagnosis of MVT.