Amegakaryocytic thrombocytopenia is an extremely rare disorder in systemic lupus erythematosus, and its mechanism and treatment are still largely unknown. We describe a 42-year-old woman with systemic lupus erythematosus who presented various clinical manifestations of life-threatening amegakaryocytic thrombocytopenia (10,000 platelets/mm3 with a marked decrease of megakaryocytes in the bone marrow), proteinuria, psychosis, refractory chylothorax, ascites, and type II diabetes caused by the anti-insulin receptor autoantibody. She was initially treated with prednisolone (25-50 mg/day) and cyclosporine A (200 mg/day) without any improvement in severe thrombocytopenia. However, her clinical symptoms, including platelet counts, dramatically improved, with a concurrent decrease in the anti-c-Mpl antibody, an autoantibody against the thrombopoietin receptor, after a subsequent treatment with rituximab (375 mg/m2 intravenously, weekly, for two consecutive weeks). Our case suggested that amegakaryocytic thrombocytopenia in patients with systemic lupus erythematosus might be mediated by the anti-c-Mpl antibody and could be treated with rituximab through elimination of pathogenic B cells producing autoimmune antibodies.