Hepatic abscesses are divided into bacterial and amoebic types. Although the prognosis of bacterial liver abscesses has improved owing to progress in drainage techniques and antimicrobial agents, poor outcomes remain common. While there have been some reports of amoebic liver abscesses complicated by thrombosis, bacterial liver abscesses and subsequent thrombus in the right atrium are very rare. We herein report the case of an 82-year-old man. He had suffered acute obstructive suppurative cholangitis 10 months previously, and bile culture yielded Enterococcus faecalis. In the present case, a right atrial thrombus caused by a bacterial liver abscess was observed and the causative organism was thought to be Enterococcus faecalis, for which was detected in a blood culture was positive. The patient was successfully treated with hepatic abscess drainage and surgical right atrial thrombectomy under cardiopulmonary bypass with a beating heart.