Background <p>The Warden procedure effectively corrects partial anomalous pulmonary venous connection (PAPVC) draining into the superior vena cava (SVC), yet superior vena cava obstruction remains a serious potential complication. This report describes a rare case of acute prosthetic graft thrombosis in the SVC following Warden procedure, presenting primarily with rapid neurological deterioration and initially lacking typical signs of superior vena cava syndrome.</p> Case presentation <p>A 51-year-old female patient underwent a Warden procedure with autologous pericardial tube reconstruction of the superior vena cava. Postoperatively, her central venous pressure (CVP) progressively increased from 12 mmHg to a peak of 28 mmHg. Concurrently, her level of consciousness deteriorated from mild coma to deep coma with brainstem reflex suppression. Emergency cranial CT revealed no hemorrhage or significant edema. The combination of elevated CVP and deteriorating neurological function suggested acute SVC obstruction, prompting emergency exploration. Intraoperatively, extensive thrombosis within the autologous pericardial graft was confirmed. After replacement with a large-bore bovine pericardial graft, venous return was restored. The patient regained consciousness 8&#xa0;h after the second surgery with no neurological sequelae.</p> Conclusions <p>Acute superior vena cava (SVC) obstruction can directly cause severe neurological dysfunction due to impaired cerebral venous return and reduced cerebral perfusion pressure. During the perioperative period, even in the absence of facial/neck edema or positive cranial CT findings, immediate investigation of superior vena cava anastomotic patency is warranted upon detection of abnormally elevated central venous pressure (CVP) accompanied by altered mental status.</p>