A 25-year-old female patient with chronic glomerulonephritis, initiated on haemodialysis presented with high-grade fever, a dysfunctional catheter, low oxygen saturation and unstable blood pressure. Upon evaluation, the patient was febrile with elevated white blood cell counts. She was intubated, started on inotropes and transferred to the intensive care unit. Chest radiography showed that the tunnelled internal jugular dialysis catheter had migrated to the inferior vena cava. Echocardiography and transoesophageal echocardiography showed severe heart dysfunction with a large thrombus attached to the catheter, indicating catheter-related atrial thrombus (CRAT). CT pulmonary angiography revealed blockage of the segmental pulmonary arteries, suggesting pulmonary embolism. Blood and tracheal cultures revealed Methicillin-resistant Staphylococcus aureus (MRSA). The patient was administered appropriate antibiotics and anticoagulants and underwent surgical removal of the thrombus and the catheter. This case demonstrates the risks associated with improper placement of dialysis catheters and highlights the brief management of CRAT.