We report the first case of successful surgical resection of a malignant phaeochromocytoma with tumour extension into vena cava and right atrium in a patient with multiple endocrine neoplasia type 2A. A 21-year-old woman with genetic confirmation of multiple endocrine neoplasia type 2A syndrome was diagnosed with a very rare case of malignant phaeochromocytoma with tumour thrombus extension into vena cava and right atrium causing Budd-Chiari syndrome. It posed a challenge to the surgeons with regard to complete tumour resection and vascular control. Reviewing the limited literature, surgical resection by means of cardiopulmonary bypass with hypothermic circulatory arrest has been reported with success in phaeochromocytoma with advance vascular involvement. Adopting this approach, adrenalectomy with complete thrombus excision by inferior vena cava exploration and right atriotomy were performed successfully by a multidisciplinary team.