This article presents a clinical case of urgent, life-saving surgical intervention in a 69-year-old woman with left atrial myxoma with rapid morphological and clinical progression and a history of COVID-19 and breast cancer in remission. However, the concurrent (perhaps secondary) thrombophilic condition facilitated the complication development in the form of superior vena caval orifice thrombosis in the early postoperative period. For this complication, repeated surgery in the volume of thrombectomy was performed, which resulted in stabilization of the patient's condition.