We report a 67-year-old woman who was diagnosed with hepatic portal venous gas associated with severe graft-versus-host disease (GVHD) of the gastrointestinal tract. The patient received allogenic peripheral blood stem cell transplantation from a haploidentical son against Philadelphia chromosome-positive acute lymphocytic leukemia. The patient developed grade 3 intestinal GVHD on day 90 from the transplantation. On day 149, she presented septic shock and computed tomography (CT) scan revealed hepatic portal venous gas (HPVG); an ileocecal resection was performed immediately. The damage of gastrointestinal mucosa by GVHD resulted in the invasion of gas-producing bacteria. Although HPVG-associated gastrointestinal GVHD is extremely rare, we should pay special attention to this pathogenesis.