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Background: Extra-hepatic portal venous obstruction (EHPVO) and liver fibrosis (or cirrhosis) are the most common causes leading to portal hypertension in children. However, we found a rare cause of portal hypertension through portal venography, the congenital absence of the right portal vein, which is also a rare portal anomaly. Methods: A 9-year-old female pediatric patient suffering from upper gastrointestinal bleeding was diagnosed with portal cavernoma based on the abdominal ultrasound (US) and computerized tomography (CT). However, the extra- and intra- hepatic portal venography showed the right portal vein could not be displayed, and the main portal vein and left portal vein were normal. The liver biopsy was normal. The absence of the right portal vein was confirmed in the patient based on the above-mentioned results. A proximal inferior mesenteric vein (IMV) to left renal vein (LRV) shunt was performed, in which the confluence of splenic vein with superior mesenteric vein was ligated, and the proximal end of inferior mesenteric vein was anastomosed with the left renal vein using a 6–0 Prolene suture. Results: The follow-up period was 8 months. The extra-hepatic portal pressure was reduced from preoperative 31 cm H2O to postoperative 22 cmH2O. The patency of the shunt was shown by the post-operative CT and US. There was no re-bleeding after surgery. The splenomegaly and esophagogastric varices were relieved shown by the postoperative US and upper gastrointestinal radiography. Conclusions: The portal venography is an important examination for portal hypertension in children, which can avoid misdiagnosis of abdominal US and CT. The proximal inferior mesenteric vein to left renal vein shunt is a feasible and effective treatment for patients with portal hypertension caused by a congenital absence of the right portal vein.