Extrahepatic portal vein obstruction (EHPVO) is a rare disease-causing form of portal hypertension. Myeloproliferative neoplasm (MPN) including essential thrombocythemia (ET) is a reported risk factor for EHPVO due to underlying persistent thrombophilia. A Japanese woman in her 40s was referred to our hospital with a 1-month history of gastric variceal bleeding due to EHPVO. Laboratory investigation showed thrombocytosis despite portal hypertension. She had a mutation in clonal marker JAK2V617F with EHPVO, which prompted us to consult a hematologist. A bone marrow biopsy revealed megakaryocyte lineage proliferation, which confirmed a diagnosis of ET. Esophagogastroduodenoscopy revealed esophagogastric varices (LsF2CbRC2, Lg-cF1RC1), and abdominal computed tomography and angiography revealed splenomegaly and portal vein thrombosis with cavernous transformation, which suggested EHPVO. The patient had a history of ruptured esophagogastric varices and required prophylaxis against further variceal bleeding before antithrombotic therapy for EHPVO with ET. We performed laparoscopic Hassab's operation followed by endoscopic variceal ligation (EVL) and hematological cytoreduction therapy. Laparoscopic Hassab's operation and three bi-monthly EVL procedures improved the esophagogastric varix (LmF0RC0, Lg-f F0RC0) at 6 months after surgery. Cytoreduction therapy reduced platelet count to 60.1 × 104/uL, and the patient was very healthy at 7 months after surgery. Patients with EHPVO are traditionally referred to a gastroenterologist for abdominal pain, intestinal bleeding, or refractory ascites; however, hypercoagulative disease may be occult in such patients and require the attention of a hematologist. When treating patients with EHPVO, gastroenterologists should screen for hematological disease, including MPN.