We describe an autopsy case of Takayasu arteritis with right atrium perforation and injuries of the right common iliac artery and vein caused by cannulation for percutaneous cardiopulmonary support (PCPS). The decedent was an 8-year-old girl admitted for examination in respect to chest pain and syncope. During catheter angiography, she suddenly went into cardiac arrest. PCPS was attempted, whereupon bleeding into the abdominal cavity and an injury to the common iliac vein were observed. She was pronounced dead 78 hours after the initiation of PCPS. Autopsy revealed thickening of the aortic wall from the ascending aorta to the abdominal aorta, with narrowing of the proximal branches. Hemopericardium induced by right atrium perforation, and an injury of the right common iliac artery, were also found. Microscopic examinations of the aorta disclosed thickening of each layer of the vessel wall and inflammatory cell infiltration, mainly into the outer layer of the media. It was speculated that manipulation of the catheter and the underlying Takayasu arteritis caused cardiac arrest. It is also considered that hypovolemia was induced by the injuries of the right common iliac artery and vein caused during the insertion of the PCPS venous cannula. In addition, the right atrium was injured by the edge of the PCPS cannula, leading to hemopericardium. In pediatric cases involving PCPS, or in cases where cannulation is difficult, regular examination of the pericardial and abdominal cavities by echocardiography would provide useful information to prevent such accidents.